From b2282eda5a8185a60105039f7c0c81cca8fabef0 Mon Sep 17 00:00:00 2001 From: NiPreps Bot Date: Mon, 25 Sep 2023 17:36:24 +0000 Subject: [PATCH] docs(master): Update docs of development line --- master/.buildinfo | 2 +- master/_modules/index.html | 14 +++--- .../sdcflows/cli/find_estimators.html | 14 +++--- master/_modules/sdcflows/data.html | 14 +++--- master/_modules/sdcflows/fieldmaps.html | 14 +++--- .../sdcflows/interfaces/brainmask.html | 14 +++--- .../_modules/sdcflows/interfaces/bspline.html | 14 +++--- master/_modules/sdcflows/interfaces/epi.html | 14 +++--- master/_modules/sdcflows/interfaces/fmap.html | 14 +++--- .../sdcflows/interfaces/reportlets.html | 14 +++--- .../_modules/sdcflows/interfaces/utils.html | 14 +++--- master/_modules/sdcflows/transform.html | 16 +++--- master/_modules/sdcflows/utils/bimap.html | 14 +++--- master/_modules/sdcflows/utils/epimanip.html | 14 +++--- master/_modules/sdcflows/utils/misc.html | 14 +++--- .../_modules/sdcflows/utils/phasemanip.html | 14 +++--- master/_modules/sdcflows/utils/tools.html | 14 +++--- master/_modules/sdcflows/utils/wrangler.html | 14 +++--- master/_modules/sdcflows/viz/utils.html | 14 +++--- .../sdcflows/workflows/ancillary.html | 14 +++--- .../sdcflows/workflows/apply/correction.html | 14 +++--- .../workflows/apply/registration.html | 14 +++--- master/_modules/sdcflows/workflows/base.html | 14 +++--- .../sdcflows/workflows/fit/fieldmap.html | 14 +++--- .../sdcflows/workflows/fit/pepolar.html | 14 +++--- .../_modules/sdcflows/workflows/fit/syn.html | 14 +++--- .../_modules/sdcflows/workflows/outputs.html | 14 +++--- master/_static/documentation_options.js | 2 +- master/api.html | 14 +++--- .../sdcflows-workflows-apply-correction-1.pdf | Bin 9688 -> 9688 bytes ...dcflows-workflows-apply-registration-1.pdf | Bin 10709 -> 10709 bytes .../api/sdcflows-workflows-fit-fieldmap-1.pdf | Bin 13242 -> 13242 bytes .../api/sdcflows-workflows-fit-fieldmap-2.pdf | Bin 8710 -> 8710 bytes .../api/sdcflows-workflows-fit-fieldmap-3.pdf | Bin 11609 -> 11609 bytes .../api/sdcflows-workflows-fit-pepolar-1.pdf | Bin 14159 -> 14159 bytes .../api/sdcflows-workflows-fit-pepolar-2.pdf | Bin 15105 -> 15105 bytes master/api/sdcflows-workflows-fit-syn-1.pdf | Bin 17715 -> 17715 bytes master/api/sdcflows-workflows-fit-syn-2.pdf | Bin 17715 -> 17715 bytes master/api/sdcflows.cli.find_estimators.html | 20 ++++---- master/api/sdcflows.cli.html | 20 ++++---- master/api/sdcflows.data.html | 20 ++++---- master/api/sdcflows.fieldmaps.html | 20 ++++---- master/api/sdcflows.interfaces.brainmask.html | 20 ++++---- master/api/sdcflows.interfaces.bspline.html | 20 ++++---- master/api/sdcflows.interfaces.epi.html | 20 ++++---- master/api/sdcflows.interfaces.fmap.html | 20 ++++---- master/api/sdcflows.interfaces.html | 20 ++++---- .../api/sdcflows.interfaces.reportlets.html | 20 ++++---- master/api/sdcflows.interfaces.utils.html | 20 ++++---- master/api/sdcflows.transform.html | 46 +++++++++--------- master/api/sdcflows.utils.bimap.html | 20 ++++---- master/api/sdcflows.utils.epimanip.html | 20 ++++---- master/api/sdcflows.utils.html | 20 ++++---- master/api/sdcflows.utils.misc.html | 20 ++++---- master/api/sdcflows.utils.phasemanip.html | 20 ++++---- master/api/sdcflows.utils.tools.html | 20 ++++---- master/api/sdcflows.utils.wrangler.html | 20 ++++---- master/api/sdcflows.viz.html | 20 ++++---- master/api/sdcflows.viz.utils.html | 20 ++++---- master/api/sdcflows.workflows.ancillary.html | 20 ++++---- .../sdcflows.workflows.apply.correction.html | 20 ++++---- master/api/sdcflows.workflows.apply.html | 20 ++++---- ...sdcflows.workflows.apply.registration.html | 20 ++++---- master/api/sdcflows.workflows.base.html | 20 ++++---- .../api/sdcflows.workflows.fit.fieldmap.html | 20 ++++---- master/api/sdcflows.workflows.fit.html | 20 ++++---- .../api/sdcflows.workflows.fit.pepolar.html | 20 ++++---- master/api/sdcflows.workflows.fit.syn.html | 20 ++++---- master/api/sdcflows.workflows.html | 20 ++++---- master/api/sdcflows.workflows.outputs.html | 20 ++++---- master/changes.html | 14 +++--- master/genindex.html | 12 ++--- master/index.html | 14 +++--- master/installation.html | 14 +++--- master/links.html | 14 +++--- master/methods.html | 14 +++--- master/objects.inv | Bin 2580 -> 2580 bytes master/py-modindex.html | 12 ++--- master/search.html | 12 ++--- master/searchindex.js | 2 +- 80 files changed, 579 insertions(+), 579 deletions(-) diff --git a/master/.buildinfo b/master/.buildinfo index 2b2a4fab8d..e2a3798938 100644 --- a/master/.buildinfo +++ b/master/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 704a8e29ece14b75b318e2607c612038 +config: 91bb20e95475d72b23f5e740bd332b15 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/master/_modules/index.html b/master/_modules/index.html index a3d8cb0c92..2f56341465 100644 --- a/master/_modules/index.html +++ b/master/_modules/index.html @@ -1,11 +1,11 @@ - + - - Overview: module code - sdcflows 2.5.2.dev74+ga6089277 documentation + + Overview: module code - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
-
sdcflows 2.5.2.dev74+ga6089277 documentation
 +
sdcflows 2.5.2.dev76+gc90c4ed5 documentation
@@ -145,14 +145,14 @@
sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
      @@ -307,7 +307,7 @@

      All modules for which code is available

    -
    +
    diff --git a/master/_modules/sdcflows/cli/find_estimators.html b/master/_modules/sdcflows/cli/find_estimators.html index 5b440155e3..513dbd5e1f 100644 --- a/master/_modules/sdcflows/cli/find_estimators.html +++ b/master/_modules/sdcflows/cli/find_estimators.html @@ -1,11 +1,11 @@ - + - - sdcflows.cli.find_estimators - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.cli.find_estimators - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
    -
    sdcflows 2.5.2.dev74+ga6089277 documentation
     +
    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
    @@ -145,14 +145,14 @@
    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
        @@ -397,7 +397,7 @@

        Source code for sdcflows.cli.find_estimators
        -
      +
      diff --git a/master/_modules/sdcflows/data.html b/master/_modules/sdcflows/data.html index 9311cb1f53..da5f9aad72 100644 --- a/master/_modules/sdcflows/data.html +++ b/master/_modules/sdcflows/data.html @@ -1,11 +1,11 @@ - + - - sdcflows.data - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.data - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
      -
      sdcflows 2.5.2.dev74+ga6089277 documentation
       +
      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
      @@ -145,14 +145,14 @@
      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
          @@ -476,7 +476,7 @@

          Source code for sdcflows.data
          -
        +
        diff --git a/master/_modules/sdcflows/fieldmaps.html b/master/_modules/sdcflows/fieldmaps.html index 0df58283c5..e3e227cb6c 100644 --- a/master/_modules/sdcflows/fieldmaps.html +++ b/master/_modules/sdcflows/fieldmaps.html @@ -1,11 +1,11 @@ - + - - sdcflows.fieldmaps - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.fieldmaps - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
        -
        sdcflows 2.5.2.dev74+ga6089277 documentation
         +
        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
        @@ -145,14 +145,14 @@
        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
            @@ -805,7 +805,7 @@

            Source code for sdcflows.fieldmaps
            -
          +
          diff --git a/master/_modules/sdcflows/interfaces/brainmask.html b/master/_modules/sdcflows/interfaces/brainmask.html index 35d2e4520f..1a515d5fa5 100644 --- a/master/_modules/sdcflows/interfaces/brainmask.html +++ b/master/_modules/sdcflows/interfaces/brainmask.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.brainmask - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.brainmask - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
          -
          sdcflows 2.5.2.dev74+ga6089277 documentation
           +
          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
          @@ -145,14 +145,14 @@
          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
              @@ -445,7 +445,7 @@

              Source code for sdcflows.interfaces.brainmask

              -
            +
            diff --git a/master/_modules/sdcflows/interfaces/bspline.html b/master/_modules/sdcflows/interfaces/bspline.html index 046190132e..2b140b0873 100644 --- a/master/_modules/sdcflows/interfaces/bspline.html +++ b/master/_modules/sdcflows/interfaces/bspline.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.bspline - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.bspline - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
            -
            sdcflows 2.5.2.dev74+ga6089277 documentation
             +
            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
            @@ -145,14 +145,14 @@
            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                @@ -987,7 +987,7 @@

                Source code for sdcflows.interfaces.bspline
                -
              +
              diff --git a/master/_modules/sdcflows/interfaces/epi.html b/master/_modules/sdcflows/interfaces/epi.html index 996b679527..18fb87904a 100644 --- a/master/_modules/sdcflows/interfaces/epi.html +++ b/master/_modules/sdcflows/interfaces/epi.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.epi - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.epi - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
              -
              sdcflows 2.5.2.dev74+ga6089277 documentation
               +
              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
              @@ -145,14 +145,14 @@
              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                  @@ -429,7 +429,7 @@

                  Source code for sdcflows.interfaces.epi
                  -
                +
                diff --git a/master/_modules/sdcflows/interfaces/fmap.html b/master/_modules/sdcflows/interfaces/fmap.html index 2a8a4c6879..8db8ef593c 100644 --- a/master/_modules/sdcflows/interfaces/fmap.html +++ b/master/_modules/sdcflows/interfaces/fmap.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.fmap - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.fmap - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                -
                sdcflows 2.5.2.dev74+ga6089277 documentation
                 +
                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                @@ -145,14 +145,14 @@
                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                    @@ -690,7 +690,7 @@

                    Source code for sdcflows.interfaces.fmap
                    -
                  +
                  diff --git a/master/_modules/sdcflows/interfaces/reportlets.html b/master/_modules/sdcflows/interfaces/reportlets.html index d01f825810..42947fd1a4 100644 --- a/master/_modules/sdcflows/interfaces/reportlets.html +++ b/master/_modules/sdcflows/interfaces/reportlets.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.reportlets - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.reportlets - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                  -
                  sdcflows 2.5.2.dev74+ga6089277 documentation
                   +
                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                  @@ -145,14 +145,14 @@
                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                      @@ -432,7 +432,7 @@

                      Source code for sdcflows.interfaces.reportlets

                      -
                    +
                    diff --git a/master/_modules/sdcflows/interfaces/utils.html b/master/_modules/sdcflows/interfaces/utils.html index db6bfa1216..47ee0175a4 100644 --- a/master/_modules/sdcflows/interfaces/utils.html +++ b/master/_modules/sdcflows/interfaces/utils.html @@ -1,11 +1,11 @@ - + - - sdcflows.interfaces.utils - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.utils - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                    -
                    sdcflows 2.5.2.dev74+ga6089277 documentation
                     +
                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                    @@ -145,14 +145,14 @@
                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                        @@ -884,7 +884,7 @@

                        Source code for sdcflows.interfaces.utils
                        -
                      +
                      diff --git a/master/_modules/sdcflows/transform.html b/master/_modules/sdcflows/transform.html index 5ab38419f0..cb6ea24b50 100644 --- a/master/_modules/sdcflows/transform.html +++ b/master/_modules/sdcflows/transform.html @@ -1,11 +1,11 @@ - + - - sdcflows.transform - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.transform - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                      -
                      sdcflows 2.5.2.dev74+ga6089277 documentation
                       +
                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                      @@ -145,14 +145,14 @@
                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                          @@ -788,7 +788,7 @@

                          Source code for sdcflows.transform

                                           self.mapped.get_fdata(dtype="float32"),  # fieldmap in Hz
                 pe_info,
                 xfms,
-                output_dtype=output_dtype,
+                output_dtype='float32',
                 order=order,
                 mode=mode,
                 cval=cval,
@@ -1092,7 +1092,7 @@ 
                          Source code for sdcflows.transform
                                 
     
   
                          
-
                          +
                        diff --git a/master/_modules/sdcflows/utils/bimap.html b/master/_modules/sdcflows/utils/bimap.html index 3e50cf4027..804b6074e2 100644 --- a/master/_modules/sdcflows/utils/bimap.html +++ b/master/_modules/sdcflows/utils/bimap.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.bimap - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.bimap - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                        -
                        sdcflows 2.5.2.dev74+ga6089277 documentation
                         +
                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                        @@ -145,14 +145,14 @@
                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                            @@ -532,7 +532,7 @@

                            Source code for sdcflows.utils.bimap
                            -
                          +
                          diff --git a/master/_modules/sdcflows/utils/epimanip.html b/master/_modules/sdcflows/utils/epimanip.html index f4bbf500dd..4572ef4a17 100644 --- a/master/_modules/sdcflows/utils/epimanip.html +++ b/master/_modules/sdcflows/utils/epimanip.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.epimanip - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.epimanip - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                          -
                          sdcflows 2.5.2.dev74+ga6089277 documentation
                           +
                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                          @@ -145,14 +145,14 @@
                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                              @@ -561,7 +561,7 @@

                              Source code for sdcflows.utils.epimanip
                              -
                            +
                            diff --git a/master/_modules/sdcflows/utils/misc.html b/master/_modules/sdcflows/utils/misc.html index e79237f6a2..965d2b1c64 100644 --- a/master/_modules/sdcflows/utils/misc.html +++ b/master/_modules/sdcflows/utils/misc.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.misc - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.misc - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                            -
                            sdcflows 2.5.2.dev74+ga6089277 documentation
                             +
                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                            @@ -145,14 +145,14 @@
                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                @@ -378,7 +378,7 @@

                                Source code for sdcflows.utils.misc
                                -
                              +
                              diff --git a/master/_modules/sdcflows/utils/phasemanip.html b/master/_modules/sdcflows/utils/phasemanip.html index 97ca612f5c..8e13996f91 100644 --- a/master/_modules/sdcflows/utils/phasemanip.html +++ b/master/_modules/sdcflows/utils/phasemanip.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.phasemanip - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.phasemanip - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                              -
                              sdcflows 2.5.2.dev74+ga6089277 documentation
                               +
                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                              @@ -145,14 +145,14 @@
                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                  @@ -445,7 +445,7 @@

                                  Source code for sdcflows.utils.phasemanip
                                  -
                                +
                                diff --git a/master/_modules/sdcflows/utils/tools.html b/master/_modules/sdcflows/utils/tools.html index e9cc55bfa5..73afdfbf67 100644 --- a/master/_modules/sdcflows/utils/tools.html +++ b/master/_modules/sdcflows/utils/tools.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.tools - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.tools - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                -
                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                 +
                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                @@ -145,14 +145,14 @@
                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                    @@ -592,7 +592,7 @@

                                    Source code for sdcflows.utils.tools
                                    -
                                  +
                                  diff --git a/master/_modules/sdcflows/utils/wrangler.html b/master/_modules/sdcflows/utils/wrangler.html index c21d2d4a80..5fec784419 100644 --- a/master/_modules/sdcflows/utils/wrangler.html +++ b/master/_modules/sdcflows/utils/wrangler.html @@ -1,11 +1,11 @@ - + - - sdcflows.utils.wrangler - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.wrangler - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                  -
                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                   +
                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                  @@ -145,14 +145,14 @@
                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                      @@ -923,7 +923,7 @@

                                      Source code for sdcflows.utils.wrangler
                                      -
                                    +
                                    diff --git a/master/_modules/sdcflows/viz/utils.html b/master/_modules/sdcflows/viz/utils.html index e76b4c6ab0..a4095c4a45 100644 --- a/master/_modules/sdcflows/viz/utils.html +++ b/master/_modules/sdcflows/viz/utils.html @@ -1,11 +1,11 @@ - + - - sdcflows.viz.utils - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.viz.utils - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                    -
                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                     +
                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                    @@ -145,14 +145,14 @@
                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                        @@ -416,7 +416,7 @@

                                        Source code for sdcflows.viz.utils
                                        -
                                      +
                                      diff --git a/master/_modules/sdcflows/workflows/ancillary.html b/master/_modules/sdcflows/workflows/ancillary.html index a22478a11c..56c4fb80c0 100644 --- a/master/_modules/sdcflows/workflows/ancillary.html +++ b/master/_modules/sdcflows/workflows/ancillary.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.ancillary - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.ancillary - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                      -
                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                       +
                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                      @@ -145,14 +145,14 @@
                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                          @@ -397,7 +397,7 @@

                                          Source code for sdcflows.workflows.ancillary
                                          -
                                        +
                                        diff --git a/master/_modules/sdcflows/workflows/apply/correction.html b/master/_modules/sdcflows/workflows/apply/correction.html index cac90a7da7..70b252173a 100644 --- a/master/_modules/sdcflows/workflows/apply/correction.html +++ b/master/_modules/sdcflows/workflows/apply/correction.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.apply.correction - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.apply.correction - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                        -
                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                         +
                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                        @@ -145,14 +145,14 @@
                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                            @@ -443,7 +443,7 @@

                                            Source code for sdcflows.workflows.apply.correction

                                            +
                                            diff --git a/master/_modules/sdcflows/workflows/apply/registration.html b/master/_modules/sdcflows/workflows/apply/registration.html index 2dc1bd9b76..ec3db09de8 100644 --- a/master/_modules/sdcflows/workflows/apply/registration.html +++ b/master/_modules/sdcflows/workflows/apply/registration.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.apply.registration - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.apply.registration - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                          -
                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                           +
                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                          @@ -145,14 +145,14 @@
                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                              @@ -439,7 +439,7 @@

                                              Source code for sdcflows.workflows.apply.registration

                                              +
                                              diff --git a/master/_modules/sdcflows/workflows/base.html b/master/_modules/sdcflows/workflows/base.html index b5214edc36..907a6d118b 100644 --- a/master/_modules/sdcflows/workflows/base.html +++ b/master/_modules/sdcflows/workflows/base.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.base - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.base - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                            -
                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                             +
                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                            @@ -145,14 +145,14 @@
                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                @@ -464,7 +464,7 @@

                                                Source code for sdcflows.workflows.base
                                                -
                                              +
                                              diff --git a/master/_modules/sdcflows/workflows/fit/fieldmap.html b/master/_modules/sdcflows/workflows/fit/fieldmap.html index 2fbbb149ba..466e4bf743 100644 --- a/master/_modules/sdcflows/workflows/fit/fieldmap.html +++ b/master/_modules/sdcflows/workflows/fit/fieldmap.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.fit.fieldmap - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.fieldmap - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                              -
                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                               +
                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                              @@ -145,14 +145,14 @@
                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                  @@ -679,7 +679,7 @@

                                                  Source code for sdcflows.workflows.fit.fieldmap

                                                  <
                                                  -
                                                +
                                                diff --git a/master/_modules/sdcflows/workflows/fit/pepolar.html b/master/_modules/sdcflows/workflows/fit/pepolar.html index f49afbe438..6f6a27b57b 100644 --- a/master/_modules/sdcflows/workflows/fit/pepolar.html +++ b/master/_modules/sdcflows/workflows/fit/pepolar.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.fit.pepolar - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.pepolar - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                                -
                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                 +
                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                @@ -145,14 +145,14 @@
                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                    @@ -730,7 +730,7 @@

                                                    Source code for sdcflows.workflows.fit.pepolar

                                                    -
                                                  +
                                                  diff --git a/master/_modules/sdcflows/workflows/fit/syn.html b/master/_modules/sdcflows/workflows/fit/syn.html index 0807338bc9..376af88c6e 100644 --- a/master/_modules/sdcflows/workflows/fit/syn.html +++ b/master/_modules/sdcflows/workflows/fit/syn.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.fit.syn - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.syn - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                                  -
                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                   +
                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                  @@ -145,14 +145,14 @@
                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                      @@ -986,7 +986,7 @@

                                                      Source code for sdcflows.workflows.fit.syn
                                                      -
                                                    +
                                                    diff --git a/master/_modules/sdcflows/workflows/outputs.html b/master/_modules/sdcflows/workflows/outputs.html index 9f7b1634ab..85ceeef0d6 100644 --- a/master/_modules/sdcflows/workflows/outputs.html +++ b/master/_modules/sdcflows/workflows/outputs.html @@ -1,11 +1,11 @@ - + - - sdcflows.workflows.outputs - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.outputs - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -123,7 +123,7 @@
                                                    -
                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                     +
                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                    @@ -145,14 +145,14 @@
                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                        @@ -632,7 +632,7 @@

                                                        Source code for sdcflows.workflows.outputs
                                                        -
                                                      +
                                                      diff --git a/master/_static/documentation_options.js b/master/_static/documentation_options.js index a9fb013d81..882642d85d 100644 --- a/master/_static/documentation_options.js +++ b/master/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '2.5.2.dev74+ga6089277', + VERSION: '2.5.2.dev76+gc90c4ed5', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/master/api.html b/master/api.html index 65baa3733b..7f60b37222 100644 --- a/master/api.html +++ b/master/api.html @@ -1,12 +1,12 @@ - + - - Library API (application program interface) - sdcflows 2.5.2.dev74+ga6089277 documentation + + Library API (application program interface) - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                      -
                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                       +
                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                      @@ -146,14 +146,14 @@
                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                          @@ -558,7 +558,7 @@

                                                          Library API (application program interface) +

                                                        diff --git a/master/api/sdcflows-workflows-apply-correction-1.pdf b/master/api/sdcflows-workflows-apply-correction-1.pdf index b56628c0e58fb4daf88baf8b49c33af37f355a82..294d6f3cd46577dcc54dd4dea82de78ad74d6d59 100644 GIT binary patch delta 22 dcmccNeZzZ$yb7nKk*T4%v6+GCW(}1Mi~v~92FU;b delta 22 dcmccNeZzZ$yb7m-}&tH5b#WNK(`Y-V7-IZR;#BLGdv25kTU delta 22 dcmZp3X>-}&tH5btXklbvYG`7-IZR;#BLGc=24w&M diff --git a/master/api/sdcflows-workflows-fit-fieldmap-3.pdf b/master/api/sdcflows-workflows-fit-fieldmap-3.pdf index ac9ddf983d71b307032c7e245d84fdb8ecf5c2ad..0cb5b952ebece4747ead938bb988bf4595687ab5 100644 GIT binary patch delta 22 dcmcZ^bu(&%ur{Zqk*T4%v6+FzW*Kc;CIDIn25*v!ym^AQVMCIDWf2VVdH delta 22 dcmZoHYb@Ka+k(@=(89>T)X>ym^AQVMCIDVw2Uh?9 diff --git a/master/api/sdcflows-workflows-fit-syn-1.pdf b/master/api/sdcflows-workflows-fit-syn-1.pdf index 4c83b9e5644aca64b802845f3fabdf1ba4b83af4..11f0d91139681b53d6610ed2461be4a4242aac60 100644 GIT binary patch delta 24 fcmdno#kjePal>0DPD>+GLvv#@L(|RQoNSo@a<~X) delta 24 fcmdno#kjePal>0DP76Z|BLh=IQ^U>QoNSo@a&!n@ diff --git a/master/api/sdcflows-workflows-fit-syn-2.pdf b/master/api/sdcflows-workflows-fit-syn-2.pdf index 616c3da3afe17a3365176317a04a7e93a041aa00..876fc24e925d9411200d29a432cba3c0c1fb9fd1 100644 GIT binary patch delta 24 fcmdno#kjePal>0DPD>+GLvv#@L-WnwoNSo@a>NK| delta 24 fcmdno#kjePal>0DP76Z|BLh=IQ{&CwoNSo@a)1b6 diff --git a/master/api/sdcflows.cli.find_estimators.html b/master/api/sdcflows.cli.find_estimators.html index 8f1c83a2e3..dd073d0f99 100644 --- a/master/api/sdcflows.cli.find_estimators.html +++ b/master/api/sdcflows.cli.find_estimators.html @@ -1,12 +1,12 @@ - + - - sdcflows.cli.find_estimators module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.cli.find_estimators module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                        -
                                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                                         +
                                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                        @@ -146,14 +146,14 @@
                                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                            @@ -251,9 +251,9 @@
                                                          -
                                                          -

                                                          sdcflows.cli.find_estimators module#

                                                          -
                                                          +
                                                          +

                                                          sdcflows.cli.find_estimators module#

                                                          +
                                                          sdcflows.cli.find_estimators.gen_layout(bids_dir, database_dir=None)[source]#
                                                          @@ -335,7 +335,7 @@

                                                          sdcflows.cli.find_estimators module +

                                                          diff --git a/master/api/sdcflows.cli.html b/master/api/sdcflows.cli.html index bfa2ccf8b1..9fcd5b31ca 100644 --- a/master/api/sdcflows.cli.html +++ b/master/api/sdcflows.cli.html @@ -1,12 +1,12 @@ - + - - sdcflows.cli package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.cli package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                          -
                                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                                           +
                                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                          @@ -146,14 +146,14 @@
                                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                              @@ -251,10 +251,10 @@
                                                            +
                                                            diff --git a/master/api/sdcflows.data.html b/master/api/sdcflows.data.html index 863a1419f6..16d10d7058 100644 --- a/master/api/sdcflows.data.html +++ b/master/api/sdcflows.data.html @@ -1,12 +1,12 @@ - + - - sdcflows.data package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.data package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                            -
                                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                                             +
                                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                            @@ -146,14 +146,14 @@
                                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                @@ -251,9 +251,9 @@
                                                              -
                                                              -

                                                              sdcflows.data package#

                                                              -

                                                              SDCFlows data files

                                                              +
                                                              +

                                                              sdcflows.data package#

                                                              +

                                                              SDCFlows data files

                                                              sdcflows.data.load(*segments) → Path#
                                                              @@ -491,7 +491,7 @@

                                                              sdcflows.data package

                                                              -
                                                              +
                                                              diff --git a/master/api/sdcflows.fieldmaps.html b/master/api/sdcflows.fieldmaps.html index bc03d94b2d..f74a876765 100644 --- a/master/api/sdcflows.fieldmaps.html +++ b/master/api/sdcflows.fieldmaps.html @@ -1,12 +1,12 @@ - + - - sdcflows.fieldmaps module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.fieldmaps module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                              -
                                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                                               +
                                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                              @@ -146,14 +146,14 @@
                                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                  @@ -251,9 +251,9 @@
                                                                -
                                                                -

                                                                sdcflows.fieldmaps module#

                                                                -

                                                                Utilities for fieldmap estimation.

                                                                +
                                                                +

                                                                sdcflows.fieldmaps module#

                                                                +

                                                                Utilities for fieldmap estimation.

                                                                class sdcflows.fieldmaps.EstimatorType(value)[source]#
                                                                @@ -587,7 +587,7 @@

                                                                sdcflows.fieldmaps module +

                                                                diff --git a/master/api/sdcflows.interfaces.brainmask.html b/master/api/sdcflows.interfaces.brainmask.html index 77c4a3d78d..89208f0107 100644 --- a/master/api/sdcflows.interfaces.brainmask.html +++ b/master/api/sdcflows.interfaces.brainmask.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.brainmask module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.brainmask module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                -
                                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                 +
                                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                @@ -146,14 +146,14 @@
                                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                    @@ -251,9 +251,9 @@
                                                                  -
                                                                  -

                                                                  sdcflows.interfaces.brainmask module#

                                                                  -

                                                                  Brain extraction interfaces.

                                                                  +
                                                                  +

                                                                  sdcflows.interfaces.brainmask module#

                                                                  +

                                                                  Brain extraction interfaces.

                                                                  class sdcflows.interfaces.brainmask.BinaryDilation(from_file=None, resource_monitor=None, **inputs)[source]#
                                                                  @@ -382,7 +382,7 @@

                                                                  sdcflows.interfaces.brainmask module +

                                                                  diff --git a/master/api/sdcflows.interfaces.bspline.html b/master/api/sdcflows.interfaces.bspline.html index 3df407e386..15b3a9fabd 100644 --- a/master/api/sdcflows.interfaces.bspline.html +++ b/master/api/sdcflows.interfaces.bspline.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.bspline module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.bspline module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                  -
                                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                   +
                                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                  @@ -146,14 +146,14 @@
                                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                      @@ -251,9 +251,9 @@
                                                                    -
                                                                    -

                                                                    sdcflows.interfaces.bspline module#

                                                                    -

                                                                    Filtering of \(B_0\) field mappings with B-Splines.

                                                                    +
                                                                    +

                                                                    sdcflows.interfaces.bspline module#

                                                                    +

                                                                    Filtering of \(B_0\) field mappings with B-Splines.

                                                                    class sdcflows.interfaces.bspline.ApplyCoeffsField(from_file=None, resource_monitor=None, **inputs)[source]#
                                                                    @@ -515,7 +515,7 @@

                                                                    sdcflows.interfaces.bspline module +

                                                                    diff --git a/master/api/sdcflows.interfaces.epi.html b/master/api/sdcflows.interfaces.epi.html index b7eafbfd56..9cdbe37e3f 100644 --- a/master/api/sdcflows.interfaces.epi.html +++ b/master/api/sdcflows.interfaces.epi.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.epi module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.epi module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                    -
                                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                     +
                                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                    @@ -146,14 +146,14 @@
                                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                        @@ -251,9 +251,9 @@
                                                                      -
                                                                      -

                                                                      sdcflows.interfaces.epi module#

                                                                      -

                                                                      Interfaces to deal with the various types of fieldmap sources.

                                                                      +
                                                                      +

                                                                      sdcflows.interfaces.epi module#

                                                                      +

                                                                      Interfaces to deal with the various types of fieldmap sources.

                                                                      class sdcflows.interfaces.epi.GetReadoutTime(from_file=None, resource_monitor=None, **inputs)[source]#
                                                                      @@ -371,7 +371,7 @@

                                                                      sdcflows.interfaces.epi module +

                                                                      diff --git a/master/api/sdcflows.interfaces.fmap.html b/master/api/sdcflows.interfaces.fmap.html index 1067312569..ddf9374baf 100644 --- a/master/api/sdcflows.interfaces.fmap.html +++ b/master/api/sdcflows.interfaces.fmap.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.fmap module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.fmap module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                      -
                                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                       +
                                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                      @@ -146,14 +146,14 @@
                                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                          @@ -251,9 +251,9 @@
                                                                        -
                                                                        -

                                                                        sdcflows.interfaces.fmap module#

                                                                        -

                                                                        Interfaces to deal with the various types of fieldmap sources.

                                                                        +
                                                                        +

                                                                        sdcflows.interfaces.fmap module#

                                                                        +

                                                                        Interfaces to deal with the various types of fieldmap sources.

                                                                        class sdcflows.interfaces.fmap.CheckB0Units(from_file=None, resource_monitor=None, **inputs)[source]#
                                                                        @@ -482,7 +482,7 @@

                                                                        sdcflows.interfaces.fmap module +

                                                                        diff --git a/master/api/sdcflows.interfaces.html b/master/api/sdcflows.interfaces.html index 54f42413e4..e86669a9ed 100644 --- a/master/api/sdcflows.interfaces.html +++ b/master/api/sdcflows.interfaces.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                        -
                                                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                         +
                                                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                        @@ -146,14 +146,14 @@
                                                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                            @@ -251,10 +251,10 @@
                                                                          -
                                                                          -

                                                                          sdcflows.interfaces package#

                                                                          +
                                                                          +

                                                                          sdcflows.interfaces package#

                                                                          -

                                                                          Submodules#

                                                                          +

                                                                          Submodules#

                                                                          diff --git a/master/api/sdcflows.interfaces.reportlets.html b/master/api/sdcflows.interfaces.reportlets.html index c383b00ecd..871365c707 100644 --- a/master/api/sdcflows.interfaces.reportlets.html +++ b/master/api/sdcflows.interfaces.reportlets.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.reportlets module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.reportlets module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                          -
                                                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                           +
                                                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                          @@ -146,14 +146,14 @@
                                                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                              @@ -251,9 +251,9 @@
                                                                            -
                                                                            -

                                                                            sdcflows.interfaces.reportlets module#

                                                                            -

                                                                            Interfaces to generate speciality reportlets.

                                                                            +
                                                                            +

                                                                            sdcflows.interfaces.reportlets module#

                                                                            +

                                                                            Interfaces to generate speciality reportlets.

                                                                            class sdcflows.interfaces.reportlets.FieldmapReportlet(**kwargs)[source]#
                                                                            @@ -360,7 +360,7 @@

                                                                            sdcflows.interfaces.reportlets module +

                                                                            diff --git a/master/api/sdcflows.interfaces.utils.html b/master/api/sdcflows.interfaces.utils.html index ff9993bfef..a4697fb118 100644 --- a/master/api/sdcflows.interfaces.utils.html +++ b/master/api/sdcflows.interfaces.utils.html @@ -1,12 +1,12 @@ - + - - sdcflows.interfaces.utils module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.interfaces.utils module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                            -
                                                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                             +
                                                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                            @@ -146,14 +146,14 @@
                                                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                @@ -251,9 +251,9 @@
                                                                              -
                                                                              -

                                                                              sdcflows.interfaces.utils module#

                                                                              -

                                                                              Utilities.

                                                                              +
                                                                              +

                                                                              sdcflows.interfaces.utils module#

                                                                              +

                                                                              Utilities.

                                                                              class sdcflows.interfaces.utils.ConvertWarp(from_file=None, resource_monitor=None, **inputs)[source]#
                                                                              @@ -556,7 +556,7 @@

                                                                              sdcflows.interfaces.utils module +

                                                                              diff --git a/master/api/sdcflows.transform.html b/master/api/sdcflows.transform.html index 36369214a2..3a99b38571 100644 --- a/master/api/sdcflows.transform.html +++ b/master/api/sdcflows.transform.html @@ -1,12 +1,12 @@ - + - - sdcflows.transform module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.transform module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                              -
                                                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                               +
                                                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                              @@ -146,14 +146,14 @@
                                                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                  @@ -251,9 +251,9 @@
                                                                                -
                                                                                -

                                                                                sdcflows.transform module#

                                                                                -

                                                                                The \(B_0\) unwarping transform formalism.

                                                                                +
                                                                                +

                                                                                sdcflows.transform module#

                                                                                +

                                                                                The \(B_0\) unwarping transform formalism.

                                                                                This module implements a data structure to represent the displacements field associated to the deformations caused by susceptibility-derived distortions. This implementation attempts to provide a single representation of such distortions independently @@ -275,7 +275,7 @@

                                                                                sdcflows.transform module
                                                                                -apply(moving: SpatialImage, pe_dir: str | Sequence[str], ro_time: float | Sequence[float], xfms: Sequence[ndarray] | None = None, xfm_data2fmap: ndarray | None = None, approx: bool = True, order: int = 3, mode: str = 'constant', cval: float = 0.0, prefilter: bool = True, output_dtype: str | dtype | None = None, num_threads: int | None = None, allow_negative: bool = False)[source]#
                                                                                +apply(moving: SpatialImage, pe_dir: str | Sequence[str], ro_time: float | Sequence[float], xfms: Sequence[ndarray] | None = None, xfm_data2fmap: ndarray | None = None, approx: bool = True, order: int = 3, mode: str = 'constant', cval: float = 0.0, prefilter: bool = True, output_dtype: str | dtype | None = None, num_threads: int | None = None, allow_negative: bool = False)[source]#

                                                                                Apply a transformation to an image, resampling on the reference spatial object.

                                                                                Handles parallelization to resample 4D images.

                                                                                @@ -290,7 +290,7 @@

                                                                                sdcflows.transform modulenumpy.ndarray) – Transform that maps coordinates on the target_reference onto the +

                                                                              • xfm_data2fmap (numpy.ndarray) – Transform that maps coordinates on the target_reference onto the fieldmap reference (that is, the linear transform through which the fieldmap can be resampled in register with the target_reference). In other words, xfm_data2fmap is the result of calling a registration tool @@ -314,7 +314,7 @@

                                                                                sdcflows.transform modulestr or dtype) – Override the output data type, instead of propagating it from the +

                                                                              • output_dtype (str or dtype) – Override the output data type, instead of propagating it from the moving image.

                                                                              • num_threads (int) – The maximum number of parallel resamplings at any given time of execution. Use this parameter to set an upper bound to memory utilization.

                                                                                • @@ -340,7 +340,7 @@

                                                                                sdcflows.transform module
                                                                                -fit(target_reference: SpatialImage, xfm_data2fmap: ndarray | None = None, approx: bool = True) → bool[source]#
                                                                                +fit(target_reference: SpatialImage, xfm_data2fmap: ndarray | None = None, approx: bool = True) → bool[source]#

                                                                                Generate the interpolation matrix (and the VSM with it).

                                                                                Implements Eq. \(\eqref{eq:1}\), interpolating \(f(\mathbf{s})\) for all voxels in the target-image’s extent.

                                                                                @@ -350,7 +350,7 @@

                                                                                sdcflows.transform moduleSpatialImage) – The image object containing a reference grid (same as that of the data to be resampled). If a 4D dataset is provided, then the fourth dimension will be dropped.

                                                                                • -

                                                                              • xfm_data2fmap (numpy.ndarray) – Transform that maps coordinates on the target_reference onto the +

                                                                              • xfm_data2fmap (numpy.ndarray) – Transform that maps coordinates on the target_reference onto the fieldmap reference (that is, the linear transform through which the fieldmap can be resampled in register with the target_reference). In other words, xfm_data2fmap is the result of calling a registration tool @@ -464,7 +464,7 @@

                                                                                sdcflows.transform module\(\beta^3\) represents the cubic B-Spline for one dimension. -The 1D B-Spline kernel implementation uses numpy.piecewise, and is based on the +The 1D B-Spline kernel implementation uses numpy.piecewise, and is based on the closed-form given by Eq. (6) of [Unser1999].

                                                                                By iterating over dimensions, the data samples that fall outside of the compact support of the tensor-product kernel associated to each control point can be filtered @@ -490,24 +490,24 @@

                                                                                sdcflows.transform moduleReturn type: -

                                                                                numpy.ndarray (\(K \times N\))

                                                                                +

                                                                                numpy.ndarray (\(K \times N\))

                                                                                • -async sdcflows.transform.unwarp_parallel(fulldataset: ndarray, coordinates: ndarray, fmap_hz: ndarray, pe_info: Sequence[Tuple[int, float]], xfms: Sequence[ndarray], order: int = 3, mode: str = 'constant', cval: float = 0.0, prefilter: bool = True, output_dtype: str | dtype | None = None, max_concurrent: int = 2) → ndarray[source]#
                                                                                +async sdcflows.transform.unwarp_parallel(fulldataset: ndarray, coordinates: ndarray, fmap_hz: ndarray, pe_info: Sequence[Tuple[int, float]], xfms: Sequence[ndarray], order: int = 3, mode: str = 'constant', cval: float = 0.0, prefilter: bool = True, output_dtype: str | dtype | None = None, max_concurrent: int = 2) → ndarray[source]#

                                                                                Unwarp an EPI dataset parallelizing across volumes.

                                                                                Parameters:
                                                                                  -

                                                                                • fulldataset (ndarray) – An array of shape (I, J, K, T), where I, J, K are the dimensions of spatial axes +

                                                                                • fulldataset (ndarray) – An array of shape (I, J, K, T), where I, J, K are the dimensions of spatial axes and T is the number of volumes. The full data array of the EPI that are wanted after correction.

                                                                                  • -

                                                                                • coordinates (ndarray) – An array of shape (3, I, J, K) array providing the voxel (index) coordinates of +

                                                                                • coordinates (ndarray) – An array of shape (3, I, J, K) array providing the voxel (index) coordinates of the reference image (i.e., interpolated points) before SDC/HMC.

                                                                                  • -

                                                                                • fmap_hz (ndarray) – An array of shape (I, J, K) containing the displacement of each voxel in voxel units.

                                                                                  • +

                                                                                • fmap_hz (ndarray) – An array of shape (I, J, K) containing the displacement of each voxel in voxel units.

                                                                                • pe_info (tuple of (int, float)) – A tuple containing the index of the phase-encoding axis in the data array and the readout time (including sign, if displacements must be reversed)

                                                                                • xfms (list of obj:~numpy.ndarray) – A list of 4×4 matrices, each one formalizing @@ -527,7 +527,7 @@

                                                                                  sdcflows.transform modulestr or dtype) – Override the output data type, instead of propagating it from the +

                                                                                • output_dtype (str or dtype) – Override the output data type, instead of propagating it from the moving image.

                                                                                • max_concurrent (int) – The maximum number of parallel resamplings at any given time of execution. Use this parameter to set an upper bound to memory utilization.

                                                                                  • @@ -538,7 +538,7 @@

                                                                                  sdcflows.transform module
                                                                                  -async sdcflows.transform.worker(data: ndarray, coordinates: ndarray, pe_info: Tuple[int, float], hmc_xfm: ndarray, func: Callable, semaphore: Semaphore) → ndarray[source]#
                                                                                  +async sdcflows.transform.worker(data: ndarray, coordinates: ndarray, pe_info: Tuple[int, float], hmc_xfm: ndarray, func: Callable, semaphore: Semaphore) → ndarray[source]#

                                                                                  Create one worker and attach it to the execution loop.

                                                                                @@ -624,7 +624,7 @@

                                                                                sdcflows.transform module +

                                                                                diff --git a/master/api/sdcflows.utils.bimap.html b/master/api/sdcflows.utils.bimap.html index bcfd9db59a..5aa4f3f07a 100644 --- a/master/api/sdcflows.utils.bimap.html +++ b/master/api/sdcflows.utils.bimap.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.bimap module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.bimap module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                -
                                                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                 +
                                                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                @@ -146,14 +146,14 @@
                                                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                    @@ -251,9 +251,9 @@
                                                                                  -
                                                                                  -

                                                                                  sdcflows.utils.bimap module#

                                                                                  -

                                                                                  A bidirectional hashmap.

                                                                                  +
                                                                                  +

                                                                                  sdcflows.utils.bimap module#

                                                                                  +

                                                                                  A bidirectional hashmap.

                                                                                  class sdcflows.utils.bimap.EstimatorRegistry(*args, **kwargs)[source]#
                                                                                  @@ -506,7 +506,7 @@

                                                                                  sdcflows.utils.bimap module +

                                                                                  diff --git a/master/api/sdcflows.utils.epimanip.html b/master/api/sdcflows.utils.epimanip.html index 08c9ca9d3f..8203c0fb3a 100644 --- a/master/api/sdcflows.utils.epimanip.html +++ b/master/api/sdcflows.utils.epimanip.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.epimanip module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.epimanip module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                  -
                                                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                   +
                                                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                  @@ -146,14 +146,14 @@
                                                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                      @@ -251,9 +251,9 @@
                                                                                    -
                                                                                    -

                                                                                    sdcflows.utils.epimanip module#

                                                                                    -

                                                                                    Manipulation of EPI data.

                                                                                    +
                                                                                    +

                                                                                    sdcflows.utils.epimanip module#

                                                                                    +

                                                                                    Manipulation of EPI data.

                                                                                    sdcflows.utils.epimanip.epi_mask(in_file, out_file=None)[source]#
                                                                                    @@ -470,7 +470,7 @@

                                                                                    sdcflows.utils.epimanip module +

                                                                                    diff --git a/master/api/sdcflows.utils.html b/master/api/sdcflows.utils.html index 6efbf1c26f..81143a74b9 100644 --- a/master/api/sdcflows.utils.html +++ b/master/api/sdcflows.utils.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                    -
                                                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                     +
                                                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                    @@ -146,14 +146,14 @@
                                                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                        @@ -251,10 +251,10 @@
                                                                                      +
                                                                                      diff --git a/master/api/sdcflows.utils.misc.html b/master/api/sdcflows.utils.misc.html index 7d25b62b7b..85cff21a45 100644 --- a/master/api/sdcflows.utils.misc.html +++ b/master/api/sdcflows.utils.misc.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.misc module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.misc module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                      -
                                                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                       +
                                                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                      @@ -146,14 +146,14 @@
                                                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                          @@ -251,9 +251,9 @@
                                                                                        -
                                                                                        -

                                                                                        sdcflows.utils.misc module#

                                                                                        -

                                                                                        Basic miscellaneous utilities.

                                                                                        +
                                                                                        +

                                                                                        sdcflows.utils.misc module#

                                                                                        +

                                                                                        Basic miscellaneous utilities.

                                                                                        sdcflows.utils.misc.create_logger(name: str, level: int = 40) → Logger[source]#
                                                                                        @@ -368,7 +368,7 @@

                                                                                        sdcflows.utils.misc module +

                                                                                        diff --git a/master/api/sdcflows.utils.phasemanip.html b/master/api/sdcflows.utils.phasemanip.html index f08ecf5332..175b3016dd 100644 --- a/master/api/sdcflows.utils.phasemanip.html +++ b/master/api/sdcflows.utils.phasemanip.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.phasemanip module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.phasemanip module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                        -
                                                                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                         +
                                                                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                        @@ -146,14 +146,14 @@
                                                                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                            @@ -251,9 +251,9 @@
                                                                                          -
                                                                                          -

                                                                                          sdcflows.utils.phasemanip module#

                                                                                          -

                                                                                          Utilities to manipulate phase and phase difference maps.

                                                                                          +
                                                                                          +

                                                                                          sdcflows.utils.phasemanip module#

                                                                                          +

                                                                                          Utilities to manipulate phase and phase difference maps.

                                                                                          sdcflows.utils.phasemanip.au2rads(in_file, newpath=None)[source]#
                                                                                          @@ -382,7 +382,7 @@

                                                                                          sdcflows.utils.phasemanip module +

                                                                                          diff --git a/master/api/sdcflows.utils.tools.html b/master/api/sdcflows.utils.tools.html index 697c6ad84b..d49a3bec40 100644 --- a/master/api/sdcflows.utils.tools.html +++ b/master/api/sdcflows.utils.tools.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.tools module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.tools module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                          -
                                                                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                           +
                                                                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                          @@ -146,14 +146,14 @@
                                                                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                              @@ -251,9 +251,9 @@
                                                                                            -
                                                                                            -

                                                                                            sdcflows.utils.tools module#

                                                                                            -

                                                                                            Image processing tools.

                                                                                            +
                                                                                            +

                                                                                            sdcflows.utils.tools module#

                                                                                            +

                                                                                            Image processing tools.

                                                                                            sdcflows.utils.tools.brain_masker(in_file, out_file=None, padding=5)[source]#
                                                                                            @@ -415,7 +415,7 @@

                                                                                            sdcflows.utils.tools module +

                                                                                            diff --git a/master/api/sdcflows.utils.wrangler.html b/master/api/sdcflows.utils.wrangler.html index d32e2baaa7..cffeda9ff3 100644 --- a/master/api/sdcflows.utils.wrangler.html +++ b/master/api/sdcflows.utils.wrangler.html @@ -1,12 +1,12 @@ - + - - sdcflows.utils.wrangler module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.utils.wrangler module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                            -
                                                                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                             +
                                                                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                            @@ -146,14 +146,14 @@
                                                                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                @@ -251,9 +251,9 @@
                                                                                              -
                                                                                              -

                                                                                              sdcflows.utils.wrangler module#

                                                                                              -

                                                                                              Find fieldmaps on the BIDS inputs for SDC.

                                                                                              +
                                                                                              +

                                                                                              sdcflows.utils.wrangler module#

                                                                                              +

                                                                                              Find fieldmaps on the BIDS inputs for SDC.

                                                                                              sdcflows.utils.wrangler.find_anatomical_estimators(*, anat_file: BIDSFile, layout: BIDSLayout, subject: str, sessions: List[str], base_entities: Dict[str, Any], suffixes: List[str]) → List[List[FieldmapFile]][source]#
                                                                                              @@ -581,7 +581,7 @@

                                                                                              sdcflows.utils.wrangler module +

                                                                                              diff --git a/master/api/sdcflows.viz.html b/master/api/sdcflows.viz.html index 167524b40d..506c7fb5ec 100644 --- a/master/api/sdcflows.viz.html +++ b/master/api/sdcflows.viz.html @@ -1,12 +1,12 @@ - + - - sdcflows.viz package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.viz package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                              -
                                                                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                               +
                                                                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                              @@ -146,14 +146,14 @@
                                                                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                  @@ -251,10 +251,10 @@
                                                                                                +
                                                                                                diff --git a/master/api/sdcflows.viz.utils.html b/master/api/sdcflows.viz.utils.html index 1197ab344b..27911e9191 100644 --- a/master/api/sdcflows.viz.utils.html +++ b/master/api/sdcflows.viz.utils.html @@ -1,12 +1,12 @@ - + - - sdcflows.viz.utils module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.viz.utils module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                -
                                                                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                 +
                                                                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                @@ -146,14 +146,14 @@
                                                                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                    @@ -251,9 +251,9 @@
                                                                                                  -
                                                                                                  -

                                                                                                  sdcflows.viz.utils module#

                                                                                                  -

                                                                                                  Visualization tooling.

                                                                                                  +
                                                                                                  +

                                                                                                  sdcflows.viz.utils module#

                                                                                                  +

                                                                                                  Visualization tooling.

                                                                                                  sdcflows.viz.utils.coolwarm_transparent(max_alpha=0.7, opaque_perc=30, transparent_perc=8)[source]#
                                                                                                  @@ -338,7 +338,7 @@

                                                                                                  sdcflows.viz.utils module +

                                                                                                  diff --git a/master/api/sdcflows.workflows.ancillary.html b/master/api/sdcflows.workflows.ancillary.html index 7b0f5fa010..cbd1d5bd58 100644 --- a/master/api/sdcflows.workflows.ancillary.html +++ b/master/api/sdcflows.workflows.ancillary.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.ancillary module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.ancillary module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                  -
                                                                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                   +
                                                                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                  @@ -146,14 +146,14 @@
                                                                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                      @@ -251,9 +251,9 @@
                                                                                                    -
                                                                                                    -

                                                                                                    sdcflows.workflows.ancillary module#

                                                                                                    -

                                                                                                    Estimate fieldmaps for SDC.

                                                                                                    +
                                                                                                    +

                                                                                                    sdcflows.workflows.ancillary module#

                                                                                                    +

                                                                                                    Estimate fieldmaps for SDC.

                                                                                                    sdcflows.workflows.ancillary.init_brainextraction_wf(name='brainextraction_wf')[source]#
                                                                                                    @@ -350,7 +350,7 @@

                                                                                                    sdcflows.workflows.ancillary module +

                                                                                                    diff --git a/master/api/sdcflows.workflows.apply.correction.html b/master/api/sdcflows.workflows.apply.correction.html index 122769b9c7..38980385c3 100644 --- a/master/api/sdcflows.workflows.apply.correction.html +++ b/master/api/sdcflows.workflows.apply.correction.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.apply.correction module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.apply.correction module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                    -
                                                                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                     +
                                                                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                    @@ -146,14 +146,14 @@
                                                                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                        @@ -251,9 +251,9 @@
                                                                                                      -
                                                                                                      -

                                                                                                      sdcflows.workflows.apply.correction module#

                                                                                                      -

                                                                                                      Applying a fieldmap given its B-Spline coefficients in Hz.

                                                                                                      +
                                                                                                      +

                                                                                                      sdcflows.workflows.apply.correction module#

                                                                                                      +

                                                                                                      Applying a fieldmap given its B-Spline coefficients in Hz.

                                                                                                      sdcflows.workflows.apply.correction.init_unwarp_wf(*, free_mem=None, omp_nthreads=1, debug=False, name='unwarp_wf')[source]#
                                                                                                      @@ -366,7 +366,7 @@

                                                                                                      sdcflows.workflows.apply.correction module +

                                                                                                      diff --git a/master/api/sdcflows.workflows.apply.html b/master/api/sdcflows.workflows.apply.html index e5aa7d7ede..25a75c5cf6 100644 --- a/master/api/sdcflows.workflows.apply.html +++ b/master/api/sdcflows.workflows.apply.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.apply package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.apply package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                      -
                                                                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                       +
                                                                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                      @@ -146,14 +146,14 @@
                                                                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                          @@ -251,10 +251,10 @@
                                                                                                        -
                                                                                                        -

                                                                                                        sdcflows.workflows.apply package#

                                                                                                        +
                                                                                                        +

                                                                                                        sdcflows.workflows.apply package#

                                                                                                        -

                                                                                                        Submodules#

                                                                                                        +

                                                                                                        Submodules#

                                                                                                        diff --git a/master/api/sdcflows.workflows.apply.registration.html b/master/api/sdcflows.workflows.apply.registration.html index db81cf02b3..dc182cc7fa 100644 --- a/master/api/sdcflows.workflows.apply.registration.html +++ b/master/api/sdcflows.workflows.apply.registration.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.apply.registration module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.apply.registration module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                        -
                                                                                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                         +
                                                                                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                        @@ -146,14 +146,14 @@
                                                                                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                            @@ -251,9 +251,9 @@
                                                                                                          -
                                                                                                          -

                                                                                                          sdcflows.workflows.apply.registration module#

                                                                                                          -

                                                                                                          Align the fieldmap reference map to the target EPI.

                                                                                                          +
                                                                                                          +

                                                                                                          sdcflows.workflows.apply.registration module#

                                                                                                          +

                                                                                                          Align the fieldmap reference map to the target EPI.

                                                                                                          The fieldmap reference map may be a magnitude image (or an EPI dataset, in the case of PEPOLAR estimation).

                                                                                                          The target EPI is the distorted dataset (or a reference thereof).

                                                                                                          @@ -370,7 +370,7 @@

                                                                                                          sdcflows.workflows.apply.registration module +

                                                                                                          diff --git a/master/api/sdcflows.workflows.base.html b/master/api/sdcflows.workflows.base.html index 37e394e369..2e02319c56 100644 --- a/master/api/sdcflows.workflows.base.html +++ b/master/api/sdcflows.workflows.base.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.base module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.base module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                          -
                                                                                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                           +
                                                                                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                          @@ -146,14 +146,14 @@
                                                                                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                              @@ -251,9 +251,9 @@
                                                                                                            -
                                                                                                            -

                                                                                                            sdcflows.workflows.base module#

                                                                                                            -

                                                                                                            Estimate fieldmaps for SDC.

                                                                                                            +
                                                                                                            +

                                                                                                            sdcflows.workflows.base module#

                                                                                                            +

                                                                                                            Estimate fieldmaps for SDC.

                                                                                                            sdcflows.workflows.base.init_fmap_preproc_wf(*, estimators, omp_nthreads, output_dir, subject, sloppy=False, debug=False, name='fmap_preproc_wf')[source]#
                                                                                                            @@ -353,7 +353,7 @@

                                                                                                            sdcflows.workflows.base module +

                                                                                                            diff --git a/master/api/sdcflows.workflows.fit.fieldmap.html b/master/api/sdcflows.workflows.fit.fieldmap.html index a1be19ae6f..97f49859c1 100644 --- a/master/api/sdcflows.workflows.fit.fieldmap.html +++ b/master/api/sdcflows.workflows.fit.fieldmap.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.fit.fieldmap module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.fieldmap module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                            -
                                                                                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                             +
                                                                                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                            @@ -146,14 +146,14 @@
                                                                                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                @@ -251,9 +251,9 @@
                                                                                                              -
                                                                                                              -

                                                                                                              sdcflows.workflows.fit.fieldmap module#

                                                                                                              -

                                                                                                              Processing phase-difference and directly measured \(B_0\) maps.

                                                                                                              +
                                                                                                              +

                                                                                                              sdcflows.workflows.fit.fieldmap module#

                                                                                                              +

                                                                                                              Processing phase-difference and directly measured \(B_0\) maps.

                                                                                                              sdcflows.workflows.fit.fieldmap.init_fmap_wf(omp_nthreads=1, sloppy=False, debug=False, mode='phasediff', name='fmap_wf')[source]#
                                                                                                              @@ -453,7 +453,7 @@

                                                                                                              sdcflows.workflows.fit.fieldmap module +

                                                                                                              diff --git a/master/api/sdcflows.workflows.fit.html b/master/api/sdcflows.workflows.fit.html index d884567d38..2568638bda 100644 --- a/master/api/sdcflows.workflows.fit.html +++ b/master/api/sdcflows.workflows.fit.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.fit package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                              -
                                                                                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                               +
                                                                                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                              @@ -146,14 +146,14 @@
                                                                                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                  @@ -251,10 +251,10 @@
                                                                                                                -
                                                                                                                -

                                                                                                                sdcflows.workflows.fit package#

                                                                                                                +
                                                                                                                +

                                                                                                                sdcflows.workflows.fit package#

                                                                                                                -

                                                                                                                Submodules#

                                                                                                                +

                                                                                                                Submodules#

                                                                                                                diff --git a/master/api/sdcflows.workflows.fit.pepolar.html b/master/api/sdcflows.workflows.fit.pepolar.html index 561f3193d9..7008fefc89 100644 --- a/master/api/sdcflows.workflows.fit.pepolar.html +++ b/master/api/sdcflows.workflows.fit.pepolar.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.fit.pepolar module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.pepolar module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                -
                                                                                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                 +
                                                                                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                @@ -146,14 +146,14 @@
                                                                                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                    @@ -251,9 +251,9 @@
                                                                                                                  -
                                                                                                                  -

                                                                                                                  sdcflows.workflows.fit.pepolar module#

                                                                                                                  -

                                                                                                                  Datasets with multiple phase encoded directions.

                                                                                                                  +
                                                                                                                  +

                                                                                                                  sdcflows.workflows.fit.pepolar module#

                                                                                                                  +

                                                                                                                  Datasets with multiple phase encoded directions.

                                                                                                                  sdcflows.workflows.fit.pepolar.init_3dQwarp_wf(omp_nthreads=1, debug=False, name='pepolar_estimate_wf')[source]#
                                                                                                                  @@ -399,7 +399,7 @@

                                                                                                                  sdcflows.workflows.fit.pepolar module +

                                                                                                                  diff --git a/master/api/sdcflows.workflows.fit.syn.html b/master/api/sdcflows.workflows.fit.syn.html index a659c3da99..9764f8b50a 100644 --- a/master/api/sdcflows.workflows.fit.syn.html +++ b/master/api/sdcflows.workflows.fit.syn.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.fit.syn module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.fit.syn module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                  -
                                                                                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                   +
                                                                                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                  @@ -146,14 +146,14 @@
                                                                                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                      @@ -251,9 +251,9 @@
                                                                                                                    -
                                                                                                                    -

                                                                                                                    sdcflows.workflows.fit.syn module#

                                                                                                                    -

                                                                                                                    Estimating the susceptibility distortions without fieldmaps.

                                                                                                                    +
                                                                                                                    +

                                                                                                                    sdcflows.workflows.fit.syn module#

                                                                                                                    +

                                                                                                                    Estimating the susceptibility distortions without fieldmaps.

                                                                                                                    sdcflows.workflows.fit.syn.init_syn_preprocessing_wf(*, debug=False, name='syn_preprocessing_wf', omp_nthreads=1, auto_bold_nss=False, t1w_inversion=False)[source]#
                                                                                                                    @@ -431,7 +431,7 @@

                                                                                                                    sdcflows.workflows.fit.syn module +

                                                                                                                    diff --git a/master/api/sdcflows.workflows.html b/master/api/sdcflows.workflows.html index 40ab9e5ec4..accafe9a80 100644 --- a/master/api/sdcflows.workflows.html +++ b/master/api/sdcflows.workflows.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows package - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows package - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                    -
                                                                                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                     +
                                                                                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                    @@ -146,14 +146,14 @@
                                                                                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                        @@ -251,10 +251,10 @@
                                                                                                                      -
                                                                                                                      -

                                                                                                                      sdcflows.workflows package#

                                                                                                                      +
                                                                                                                      +

                                                                                                                      sdcflows.workflows package#

                                                                                                                      -

                                                                                                                      Subpackages#

                                                                                                                      +

                                                                                                                      Subpackages#

                                                                                                                      diff --git a/master/api/sdcflows.workflows.outputs.html b/master/api/sdcflows.workflows.outputs.html index ef03cf1c34..3cc4e9de2d 100644 --- a/master/api/sdcflows.workflows.outputs.html +++ b/master/api/sdcflows.workflows.outputs.html @@ -1,12 +1,12 @@ - + - - sdcflows.workflows.outputs module - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows.workflows.outputs module - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                      -
                                                                                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                       +
                                                                                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                      @@ -146,14 +146,14 @@
                                                                                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                          @@ -251,9 +251,9 @@
                                                                                                                        -
                                                                                                                        -

                                                                                                                        sdcflows.workflows.outputs module#

                                                                                                                        -

                                                                                                                        Writing out outputs.

                                                                                                                        +
                                                                                                                        +

                                                                                                                        sdcflows.workflows.outputs module#

                                                                                                                        +

                                                                                                                        Writing out outputs.

                                                                                                                        class sdcflows.workflows.outputs.DerivativesDataSink(allowed_entities=None, out_path_base=None, **inputs)[source]#
                                                                                                                        @@ -420,7 +420,7 @@

                                                                                                                        sdcflows.workflows.outputs module +

                                                                                                                        diff --git a/master/changes.html b/master/changes.html index 12cd9c4347..5aa520630f 100644 --- a/master/changes.html +++ b/master/changes.html @@ -1,12 +1,12 @@ - + - - What’s new? - sdcflows 2.5.2.dev74+ga6089277 documentation + + What’s new? - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                        -
                                                                                                                        sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                         +
                                                                                                                        sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                        @@ -146,14 +146,14 @@
                                                                                                                        sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                        • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                            @@ -939,7 +939,7 @@

                                                                                                                            0.1.0 (July 22, 2019) +

                                                                                                                          diff --git a/master/genindex.html b/master/genindex.html index 035dad73a5..89b4d9333d 100644 --- a/master/genindex.html +++ b/master/genindex.html @@ -1,10 +1,10 @@ - + - Index - sdcflows 2.5.2.dev74+ga6089277 documentation + Index - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -122,7 +122,7 @@
                                                                                                                          -
                                                                                                                          sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                           +
                                                                                                                          sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                          @@ -144,14 +144,14 @@
                                                                                                                          sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                          • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                              @@ -972,7 +972,7 @@

                                                                                                                              W

                                                                                                                            -
                                                                                                                            +
                                                                                                                            diff --git a/master/index.html b/master/index.html index 95c3fdd50b..1770159da9 100644 --- a/master/index.html +++ b/master/index.html @@ -1,12 +1,12 @@ - + - - sdcflows 2.5.2.dev74+ga6089277 documentation + + sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                            -
                                                                                                                            sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                             +
                                                                                                                            sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                            @@ -146,14 +146,14 @@
                                                                                                                            sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                            • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                @@ -442,7 +442,7 @@

                                                                                                                                Contents

                                                                                                                              -
                                                                                                                              +
                                                                                                                              diff --git a/master/installation.html b/master/installation.html index 058c222433..bf127661e6 100644 --- a/master/installation.html +++ b/master/installation.html @@ -1,12 +1,12 @@ - + - - Installation - sdcflows 2.5.2.dev74+ga6089277 documentation + + Installation - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                              -
                                                                                                                              sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                               +
                                                                                                                              sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                              @@ -146,14 +146,14 @@
                                                                                                                              sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                              • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                  @@ -352,7 +352,7 @@

                                                                                                                                  External Dependencies

                                                                                                                                -
                                                                                                                                +
                                                                                                                                diff --git a/master/links.html b/master/links.html index 58dfefb06a..40efa84a62 100644 --- a/master/links.html +++ b/master/links.html @@ -1,12 +1,12 @@ - + - - <no title> - sdcflows 2.5.2.dev74+ga6089277 documentation + + <no title> - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                                -
                                                                                                                                sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                                 +
                                                                                                                                sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                                @@ -146,14 +146,14 @@
                                                                                                                                sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                    @@ -283,7 +283,7 @@
                                                                                                                                  -
                                                                                                                                  +
                                                                                                                                  diff --git a/master/methods.html b/master/methods.html index 1f57366b78..53ff53af87 100644 --- a/master/methods.html +++ b/master/methods.html @@ -1,12 +1,12 @@ - + - - Methods and implementation - sdcflows 2.5.2.dev74+ga6089277 documentation + + Methods and implementation - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -124,7 +124,7 @@
                                                                                                                                  -
                                                                                                                                  sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                                   +
                                                                                                                                  sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                                  @@ -146,14 +146,14 @@
                                                                                                                                  sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                  • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                      @@ -636,7 +636,7 @@

                                                                                                                                      References +

                                                                                                                                    diff --git a/master/objects.inv b/master/objects.inv index 513b65db8763596104e3a1f0f20ec91d3f9b7264..270e94ea6e033245a8010a4f4bd8c31cb0525d9c 100644 GIT binary patch delta 12 TcmbOtGDT#98>87q_p_V;8x904 delta 12 TcmbOtGDT#98>7ia_p_V;8w3O@ diff --git a/master/py-modindex.html b/master/py-modindex.html index 43fa389e77..7f187570b2 100644 --- a/master/py-modindex.html +++ b/master/py-modindex.html @@ -1,10 +1,10 @@ - + - Python Module Index - sdcflows 2.5.2.dev74+ga6089277 documentation + Python Module Index - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -122,7 +122,7 @@
                                                                                                                                    -
                                                                                                                                    sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                                     +
                                                                                                                                    sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                                    @@ -144,14 +144,14 @@
                                                                                                                                    sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                    • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                        @@ -492,7 +492,7 @@

                                                                                                                                        Python Module Index

                                                                                                                                      -
                                                                                                                                      +
                                                                                                                                      diff --git a/master/search.html b/master/search.html index 7c6e7ec97d..b6c00cf4ac 100644 --- a/master/search.html +++ b/master/search.html @@ -1,10 +1,10 @@ - + - Search - sdcflows 2.5.2.dev74+ga6089277 documentation + Search - sdcflows 2.5.2.dev76+gc90c4ed5 documentation @@ -121,7 +121,7 @@
                                                                                                                                      -
                                                                                                                                      sdcflows 2.5.2.dev74+ga6089277 documentation
                                                                                                                                       +
                                                                                                                                      sdcflows 2.5.2.dev76+gc90c4ed5 documentation
                                                                                                                                      @@ -143,14 +143,14 @@
                                                                                                                                      sdcflows - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                      • - 2.5.2.dev74 (dev) + 2.5.2.dev76 (dev)
                                                                                                                                          @@ -290,7 +290,7 @@
                                                                                                                                        -
                                                                                                                                        +
                                                                                                                                        diff --git a/master/searchindex.js b/master/searchindex.js index 5f7e2cbd2a..4e49e8320b 100644 --- a/master/searchindex.js +++ b/master/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api", "api/sdcflows.cli", "api/sdcflows.cli.find_estimators", "api/sdcflows.data", "api/sdcflows.fieldmaps", "api/sdcflows.interfaces", "api/sdcflows.interfaces.brainmask", "api/sdcflows.interfaces.bspline", "api/sdcflows.interfaces.epi", "api/sdcflows.interfaces.fmap", "api/sdcflows.interfaces.reportlets", "api/sdcflows.interfaces.utils", "api/sdcflows.transform", "api/sdcflows.utils", "api/sdcflows.utils.bimap", "api/sdcflows.utils.epimanip", "api/sdcflows.utils.misc", "api/sdcflows.utils.phasemanip", "api/sdcflows.utils.tools", "api/sdcflows.utils.wrangler", "api/sdcflows.viz", "api/sdcflows.viz.utils", "api/sdcflows.workflows", "api/sdcflows.workflows.ancillary", "api/sdcflows.workflows.apply", "api/sdcflows.workflows.apply.correction", "api/sdcflows.workflows.apply.registration", "api/sdcflows.workflows.base", "api/sdcflows.workflows.fit", "api/sdcflows.workflows.fit.fieldmap", "api/sdcflows.workflows.fit.pepolar", "api/sdcflows.workflows.fit.syn", "api/sdcflows.workflows.outputs", "changes", "index", "installation", "links", "methods"], "filenames": ["api.rst", "api/sdcflows.cli.rst", "api/sdcflows.cli.find_estimators.rst", "api/sdcflows.data.rst", "api/sdcflows.fieldmaps.rst", "api/sdcflows.interfaces.rst", "api/sdcflows.interfaces.brainmask.rst", "api/sdcflows.interfaces.bspline.rst", "api/sdcflows.interfaces.epi.rst", "api/sdcflows.interfaces.fmap.rst", "api/sdcflows.interfaces.reportlets.rst", "api/sdcflows.interfaces.utils.rst", "api/sdcflows.transform.rst", "api/sdcflows.utils.rst", "api/sdcflows.utils.bimap.rst", "api/sdcflows.utils.epimanip.rst", "api/sdcflows.utils.misc.rst", "api/sdcflows.utils.phasemanip.rst", "api/sdcflows.utils.tools.rst", "api/sdcflows.utils.wrangler.rst", "api/sdcflows.viz.rst", "api/sdcflows.viz.utils.rst", "api/sdcflows.workflows.rst", "api/sdcflows.workflows.ancillary.rst", "api/sdcflows.workflows.apply.rst", "api/sdcflows.workflows.apply.correction.rst", "api/sdcflows.workflows.apply.registration.rst", "api/sdcflows.workflows.base.rst", "api/sdcflows.workflows.fit.rst", "api/sdcflows.workflows.fit.fieldmap.rst", "api/sdcflows.workflows.fit.pepolar.rst", "api/sdcflows.workflows.fit.syn.rst", "api/sdcflows.workflows.outputs.rst", "changes.rst", "index.rst", "installation.rst", "links.rst", "methods.rst"], "titles": ["Library API (application program interface)", "sdcflows.cli package", "sdcflows.cli.find_estimators module", "sdcflows.data package", "sdcflows.fieldmaps module", "sdcflows.interfaces package", "sdcflows.interfaces.brainmask module", "sdcflows.interfaces.bspline module", "sdcflows.interfaces.epi module", "sdcflows.interfaces.fmap module", "sdcflows.interfaces.reportlets module", "sdcflows.interfaces.utils module", "sdcflows.transform module", "sdcflows.utils package", "sdcflows.utils.bimap module", "sdcflows.utils.epimanip module", "sdcflows.utils.misc module", "sdcflows.utils.phasemanip module", "sdcflows.utils.tools module", "sdcflows.utils.wrangler module", "sdcflows.viz package", "sdcflows.viz.utils module", "sdcflows.workflows package", "sdcflows.workflows.ancillary module", "sdcflows.workflows.apply package", "sdcflows.workflows.apply.correction module", "sdcflows.workflows.apply.registration module", "sdcflows.workflows.base module", "sdcflows.workflows.fit package", "sdcflows.workflows.fit.fieldmap module", "sdcflows.workflows.fit.pepolar module", "sdcflows.workflows.fit.syn module", "sdcflows.workflows.outputs module", "What\u2019s new?", "SDCFlows", "Installation", "<no title>", "Methods and implementation"], "terms": {"inform": [0, 33, 37], "specif": [0, 3, 4, 33, 34], "function": [0, 3, 12, 18, 19, 31, 33, 35, 37], "class": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 32], "method": [0, 3, 4, 12, 19, 29, 30, 31, 33, 34], "sdcflow": [0, 35, 37], "cli": [0, 33, 34], "packag": [0, 33, 34, 35], "submodul": [0, 33, 34, 37], "find_estim": [0, 1, 19, 37], "modul": [0, 1, 3, 5, 13, 20, 22, 24, 28, 33, 34], "gen_layout": [0, 2], "main": [0, 2], "data": [0, 4, 6, 7, 8, 11, 12, 15, 18, 19, 32, 33, 34], "load": [0, 3, 33, 34], "readabl": [0, 3], "as_path": [0, 3], "cach": [0, 3, 12, 33], "loader": [0, 3, 34], "fieldmap": [0, 7, 8, 9, 10, 12, 14, 17, 19, 23, 25, 26, 27, 28, 30, 31, 32, 33, 34], "estimatortyp": [0, 4, 19, 34], "anat": [0, 4, 19], "map": [0, 4, 7, 9, 11, 12, 14, 17, 19, 23, 25, 26, 29, 31, 32, 33, 34], "pepolar": [0, 4, 7, 19, 26, 28, 33, 34], "phasediff": [0, 4, 7, 9, 19, 29, 33, 37], "unknown": [0, 4], "fieldmapestim": [0, 4, 14, 19, 27, 33, 34], "bids_id": [0, 4, 19], "get_workflow": [0, 4], "path": [0, 3, 4, 7, 12, 16, 29, 30, 31, 32, 33, 35], "sourc": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 29, 30, 31, 32, 34, 37], "fieldmapfil": [0, 4, 19, 33, 34], "bids_root": [0, 4], "check_path": [0, 4], "entiti": [0, 4, 19, 32, 33], "find_meta": [0, 4], "metadata": [0, 4, 8, 9, 11, 12, 15, 17, 19, 25, 29, 30, 31, 32, 33, 37], "suffix": [0, 4, 19], "metadataerror": [0, 4, 34], "clear_registri": [0, 4, 19, 34], "get_identifi": [0, 4, 34], "brainmask": [0, 5, 23, 31], "binarydil": [0, 6], "brainextract": [0, 6], "union": [0, 6], "bspline": [0, 5, 33, 37], "applycoeffsfield": [0, 7, 33], "bsplineapprox": [0, 7, 33], "topupcoeffreori": [0, 7], "transformcoeffici": [0, 7], "bspline_grid": [0, 7], "epi": [0, 5, 6, 7, 11, 12, 15, 18, 19, 23, 25, 26, 30, 31, 33, 34, 37], "getreadouttim": [0, 8], "sortpeblip": [0, 8], "fmap": [0, 3, 4, 5, 26, 27, 29, 30, 31], "checkb0unit": [0, 9], "checkregist": [0, 9], "displacementsfield2fieldmap": [0, 9], "phasemap2rad": [0, 9], "phasediff2fieldmap": [0, 9], "subtractphas": [0, 9], "reportlet": [0, 5, 33], "fieldmapreportlet": [0, 10, 33], "util": [0, 4, 5, 12, 20, 33, 34, 37], "convertwarp": [0, 11], "denoiseimag": [0, 11], "deobliqu": [0, 11, 37], "flatten": [0, 11, 14, 30], "padslic": [0, 11], "positivedirectioncosin": [0, 11], "reobliqu": [0, 11], "reorientimageandmetadata": [0, 11], "uniformgrid": [0, 11], "transform": [0, 7, 9, 18, 26, 31, 34, 37], "b0fieldtransform": [0, 7, 12, 34], "appli": [0, 7, 12, 19, 22, 29, 30, 31, 33, 37], "coeff": [0, 12], "fit": [0, 7, 12, 22, 33, 37], "to_displac": [0, 12], "disp_to_fmap": [0, 12, 34], "fmap_to_disp": [0, 12, 34], "grid_bspline_weight": [0, 7, 12, 34], "unwarp_parallel": [0, 12, 34], "worker": [0, 12, 34], "bimap": [0, 13], "estimatorregistri": [0, 14], "get_kei": [0, 14], "bidict": [0, 14], "add": [0, 11, 14, 33], "clear": [0, 14, 37], "epimanip": [0, 13], "epi_mask": [0, 15, 31], "get_trt": [0, 15], "misc": [0, 13], "create_logg": [0, 16], "front": [0, 16, 33, 37], "get_free_mem": [0, 16], "last": [0, 4, 14, 15, 16, 17, 33], "phasemanip": [0, 13], "au2rad": [0, 17], "delta_t": [0, 17], "phdiff2fmap": [0, 17], "subtract_phas": [0, 17], "tool": [0, 12, 13, 21, 33, 34, 35], "brain_mask": [0, 18], "deoblique_and_zoom": [0, 18], "ensure_positive_cosin": [0, 18], "reorient_pedir": [0, 18], "resample_to_zoom": [0, 18], "wrangler": [0, 13, 33, 37], "find_anatomical_estim": [0, 19], "viz": [0, 34], "coolwarm_transpar": [0, 21], "plot_registr": [0, 21], "workflow": [0, 4, 19, 33, 34, 37], "subpackag": [0, 34], "correct": [0, 7, 11, 12, 24, 29, 33, 34, 37], "init_unwarp_wf": [0, 25], "registr": [0, 9, 10, 12, 24, 31, 33, 34], "init_coeff2epi_wf": [0, 26], "init_fmap_wf": [0, 29], "init_magnitude_wf": [0, 29], "init_phdiff_wf": [0, 29], "init_3dqwarp_wf": [0, 30], "init_topup_wf": [0, 30, 33], "syn": [0, 7, 11, 28, 33, 37], "init_syn_preprocessing_wf": [0, 31, 37], "init_syn_sdc_wf": [0, 31, 37], "match_histogram": [0, 31], "ancillari": [0, 22], "init_brainextraction_wf": [0, 23], "base": [0, 4, 6, 7, 8, 9, 10, 11, 12, 14, 22, 29, 30, 31, 32, 34, 35, 37], "init_fmap_preproc_wf": [0, 27, 33], "output": [0, 6, 7, 8, 9, 10, 11, 12, 22, 23, 25, 26, 27, 29, 30, 31, 33, 37], "derivativesdatasink": [0, 32, 33], "out_path_bas": [0, 32], "init_fmap_derivatives_wf": [0, 32], "init_fmap_reports_wf": [0, 32], "bids_dir": 2, "database_dir": 2, "none": [2, 4, 6, 7, 8, 9, 11, 12, 14, 15, 17, 18, 19, 21, 25, 31, 32, 37], "argv": 2, "pars": 2, "bid": [2, 4, 8, 9, 15, 17, 19, 29, 32, 33, 34], "directori": [2, 3, 27, 32], "print": [2, 35], "subject": [2, 19, 27, 33], "estim": [2, 4, 7, 11, 12, 14, 19, 23, 26, 27, 29, 30, 31, 32, 33, 34], "file": [3, 4, 6, 7, 8, 9, 10, 11, 12, 19, 23, 26, 30, 31, 32, 33, 35], "segment": [3, 37], "rel": [3, 33, 35], "thi": [3, 4, 7, 9, 11, 12, 15, 18, 19, 25, 26, 27, 29, 30, 31, 33, 34, 37], "contain": [3, 12, 14, 19, 29, 30, 32, 33, 37], "follow": [3, 7, 12, 15, 18, 33, 35, 37], "top": 3, "level": [3, 12, 16, 19, 33, 37], "affin": [3, 7, 9, 12, 33], "json": [3, 4, 15], "flirtsch": 3, "any_registr": 3, "any_registration_test": 3, "fmap_atla": 3, "nii": [3, 4, 9, 15, 29], "gz": [3, 4, 9, 15, 29], "fmap_atlas_2_mni152nlin2009casym_affin": 3, "mat": 3, "sd_syn": 3, "sd_syn_sloppi": 3, "translation_rigid": 3, "travers": 3, "provid": [3, 4, 12, 15, 19, 29, 33, 34, 37], "read": [3, 4, 17], "access": [3, 33, 34], "resourc": [3, 33], "through": [3, 7, 9, 11, 12, 33], "like": [3, 12, 31], "interfac": [3, 4, 18, 33, 34, 37], "mai": [3, 4, 7, 9, 12, 15, 25, 26, 27, 29, 34, 37], "exist": [3, 6, 7, 8, 9, 10, 11, 32, 37], "filesystem": 3, "effici": [3, 33], "us": [3, 4, 7, 9, 11, 12, 15, 18, 19, 25, 26, 27, 29, 31, 33, 35, 37], "oper": [3, 12, 15, 18, 33], "includ": [3, 12, 19, 33, 37], "result": [3, 7, 12, 33, 37], "i": [3, 4, 7, 8, 9, 11, 12, 14, 15, 18, 19, 21, 26, 29, 31, 33, 34, 35, 37], "copi": [3, 11, 33], "case": [3, 7, 9, 19, 26, 33, 37], "where": [3, 7, 9, 10, 12, 15, 31, 37], "would": 3, "necessari": [3, 11, 15, 19, 29, 33, 37], "abstractcontextmanag": 3, "ensur": [3, 9, 11, 29, 33], "avail": [3, 4, 8, 15, 19, 33, 35, 37], "gener": [3, 7, 9, 10, 12, 14, 18, 26, 27, 29, 33], "context": [3, 33], "manag": 3, "yield": [3, 37], "when": [3, 4, 7, 12, 19, 29, 33, 37], "enter": 3, "ani": [3, 8, 9, 11, 12, 19, 32, 37], "temporari": [3, 12], "ar": [3, 4, 7, 8, 9, 11, 12, 15, 18, 19, 29, 30, 31, 32, 33, 34, 35, 37], "creat": [3, 7, 12, 19, 27, 30, 31, 33], "delet": 3, "exit": 3, "remain": 3, "throughout": 3, "durat": 3, "program": [3, 11, 33, 34], "python": [3, 33, 34, 35], "so": [3, 7, 8, 9, 31, 33, 37], "multipl": [3, 30, 33, 37], "call": [3, 4, 7, 12, 14, 15, 17, 25, 33], "do": [3, 12, 15, 33, 37], "unpack": 3, "same": [3, 7, 9, 11, 12, 33, 37], "time": [3, 7, 8, 9, 11, 12, 15, 25, 33, 37], "sensit": [3, 33], "argument": [3, 4, 11, 19, 33, 37], "": [3, 4, 7, 8, 9, 11, 12, 14, 15, 19, 25, 29, 30, 31, 32, 34, 35, 37], "pass": [3, 9, 18, 19, 33, 37], "anchor": 3, "str": [3, 4, 11, 12, 16, 19, 23, 25, 26, 27, 29, 30, 31, 32], "A": [3, 4, 7, 10, 11, 12, 14, 18, 19, 27, 29, 30, 31, 32, 33, 35, 37], "wrap": [3, 9, 11, 12, 29, 37], "importlib": 3, "getter": 3, "an": [3, 6, 7, 8, 9, 10, 11, 12, 14, 15, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37], "interpret": [3, 35, 37], "lifetim": 3, "scope": 3, "For": [3, 12, 15, 18, 19, 29, 37], "typic": [3, 12, 34, 37], "simpli": 3, "object": [3, 4, 6, 7, 8, 9, 10, 11, 12, 19, 32, 33], "zip": 3, "distribut": [3, 7], "clean": [3, 19], "up": [3, 25, 31, 32, 33, 35, 37], "accept": [3, 18, 33], "fulli": [3, 7, 18], "qualifi": 3, "name": [3, 4, 10, 15, 16, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33], "expect": [3, 9, 11, 31], "usag": 3, "autofunct": 3, "load_data": 3, "automethod": 3, "from": [3, 4, 7, 8, 9, 11, 12, 15, 16, 17, 18, 19, 23, 25, 29, 31, 32, 33, 35, 37], "import": [3, 18, 19, 33, 35], "__package__": 3, "implement": [3, 7, 12, 15, 33, 34], "callabl": [3, 12], "docstr": [3, 33], "intend": [3, 11], "treat": [3, 11], "document": [3, 15, 33], "greater": 3, "flexibl": [3, 37], "improv": [3, 33], "over": [3, 12, 15, 33], "explicit": [3, 34], "On": [3, 35], "true": [3, 4, 7, 9, 11, 12, 14, 18, 19, 31, 32, 37], "fals": [3, 4, 7, 9, 10, 11, 12, 19, 21, 25, 26, 27, 29, 30, 31, 32], "n": [3, 11, 12, 37], "It": [3, 15, 37], "also": [3, 7, 19, 25, 31, 33, 37], "possibl": [3, 15, 19, 37], "directli": [3, 7, 12, 29, 33, 37], "other_packag": 3, "ext": 3, "read_text": 3, "pkgdata": 3, "requir": [3, 29, 33, 34, 35], "full": [3, 12, 21], "func": [3, 12], "contrast": [3, 31], "importlib_resourc": 3, "as_fil": 3, "joinpath": 3, "valu": [4, 6, 7, 8, 9, 10, 11, 12, 14, 19, 32, 33], "enum": 4, "repres": [4, 6, 7, 8, 9, 10, 11, 12, 32, 37], "differ": [4, 9, 15, 17, 19, 29, 33, 34], "type": [4, 8, 9, 12, 14, 19, 32, 37], "approach": [4, 19, 33, 34], "5": [4, 7, 12, 18, 19, 34, 35, 37], "4": [4, 7, 11, 12, 14, 15, 18, 19, 34, 37], "2": [4, 7, 9, 11, 12, 14, 15, 19, 34, 35, 37], "3": [4, 6, 7, 11, 12, 14, 15, 18, 19, 31, 34, 35, 37], "1": [4, 7, 9, 10, 11, 12, 14, 15, 16, 18, 19, 25, 29, 30, 31, 34, 35, 37], "strategi": [4, 7, 12, 27, 33, 37], "consist": [4, 8, 9, 11, 33, 37], "all": [4, 7, 9, 11, 12, 14, 18, 19, 33, 35], "The": [4, 6, 7, 9, 11, 12, 15, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37], "actual": [4, 7, 25, 29], "infer": [4, 11], "input": [4, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 37], "collect": [4, 33], "uniqu": [4, 25, 26, 29], "b0fieldidentifi": [4, 19, 27, 32, 33, 34], "field": [4, 7, 9, 11, 12, 15, 19, 25, 26, 27, 29, 30, 31, 32, 33, 37], "kwarg": [4, 10, 14], "build": [4, 31, 32, 33, 35, 37], "correspond": [4, 7, 8, 9, 11, 19, 25, 26, 29, 30, 31, 33, 34, 37], "instanc": [4, 18, 19, 33, 37], "flag": 4, "indic": [4, 11, 19], "return": [4, 12, 14, 16, 18, 19, 33], "tupl": [4, 7, 11, 12, 16, 29, 31], "sort": [4, 8, 23, 33], "list": [4, 7, 8, 9, 11, 12, 14, 16, 19, 25, 27, 29, 30, 31, 32], "noth": 4, "bool": [4, 12, 19, 25, 26, 27, 29, 30, 31, 32], "can": [4, 7, 11, 12, 15, 18, 19, 26, 29, 35, 37], "some": [4, 15, 19, 23, 29, 33, 35, 37], "sidecar": [4, 15], "filenam": [4, 10, 11, 32], "match": [4, 7, 31], "receiv": [4, 37], "keyword": 4, "initi": [4, 19, 33], "exampl": [4, 14, 16, 17, 19], "f": [4, 7, 12, 15, 17, 33], "dsa_dir": 4, "sub": 4, "01": [4, 7, 19, 34], "01_t1w": 4, "t1w": [4, 19, 31, 33, 37], "01_dir": 4, "lr_epi": 4, "traceback": [4, 14, 15, 17], "most": [4, 12, 14, 15, 17, 18, 33, 37], "recent": [4, 7, 14, 15, 17, 29], "totalreadouttim": [4, 15], "0": [4, 7, 9, 10, 11, 12, 15, 16, 17, 18, 21, 25, 29, 30, 31, 34, 35, 37], "005": 4, "006": 4, "01_phasediff": 4, "echotime2": [4, 17, 29], "00746": 4, "01_phase2": 4, "echotim": [4, 29], "01_fieldmap": 4, "unit": [4, 9, 12, 17, 25, 29, 32, 33], "rad": [4, 9, 17, 33], "root": [4, 7, 33], "attribut": 4, "valid": [4, 12, 15, 19, 33], "extract": [4, 6, 11, 23, 32, 33], "filepath": 4, "enabl": [4, 7, 27, 33], "disabl": 4, "autom": [4, 37], "search": [4, 19, 37], "associ": [4, 12, 19, 31, 37], "overwrit": 4, "except": [4, 19], "valueerror": [4, 14, 15, 17], "better": [4, 15, 33], "error": [4, 7, 15, 33, 37], "empti": [4, 11, 14, 19], "registri": [4, 19, 33], "intendedfor": [4, 19, 33, 34], "identifi": [4, 12, 19, 33, 37], "given": [4, 9, 12, 17, 19, 23, 25, 30, 31, 33, 37], "paramet": [4, 9, 11, 12, 15, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 37], "we": [4, 7, 9, 12, 19, 29, 33, 37], "want": [4, 12, 37], "index": [4, 11, 12, 30], "tabl": 4, "which": [4, 7, 8, 9, 11, 12, 15, 27, 30, 32, 33, 37], "should": [4, 9, 10, 11, 12, 15, 18, 19, 29, 30, 31, 32, 33, 37], "perform": [4, 18, 26, 33, 37], "brain": [6, 7, 9, 10, 15, 23, 26, 29, 31, 32, 33, 37], "from_fil": [6, 7, 8, 9, 11], "resource_monitor": [6, 7, 8, 9, 11], "simpleinterfac": [6, 7, 8, 9, 11], "gre": [6, 23, 29, 37], "mandatori": [6, 7, 8, 9, 10, 11, 19, 32], "in_fil": [6, 8, 9, 11, 15, 17, 18, 23, 32], "pathlik": [6, 7, 8, 9, 10, 11, 12, 29, 32], "string": [6, 7, 8, 9, 10, 11, 19, 32], "binari": [6, 11, 29, 35], "dilat": 6, "option": [6, 7, 8, 9, 10, 11, 12, 15, 19, 23, 27, 30, 31, 32, 33, 37], "radiu": [6, 9], "float": [6, 7, 8, 9, 10, 12, 18, 31], "structur": [6, 12, 19, 33, 37], "element": [6, 16, 30, 31], "ball": 6, "nipyp": [6, 7, 9, 10, 11, 32, 33, 34, 35], "default": [6, 7, 9, 10, 11, 12, 21, 23, 27, 29, 32, 33, 37], "out_fil": [6, 9, 11, 15, 18, 23, 32], "after": [6, 7, 11, 12, 19, 23, 25, 29, 30, 33], "mask": [6, 7, 10, 11, 15, 18, 23, 25, 26, 29, 30, 31, 32, 33], "out_mask": [6, 11, 23], "out_probseg": [6, 23], "probabilist": 6, "in1": 6, "in2": 6, "filter": [7, 12, 19, 33, 37], "b_0": [7, 12, 15, 29, 33, 37], "b": [7, 12, 14, 18, 19, 23, 25, 29, 30, 31, 33, 37], "spline": [7, 12, 23, 25, 29, 30, 31, 33, 37], "undistort": 7, "target": [7, 12, 18, 25, 26, 32, 33, 37], "distort": [7, 12, 19, 25, 26, 31, 33, 34], "imag": [7, 8, 9, 11, 12, 15, 18, 19, 23, 25, 26, 29, 31, 33, 34], "formal": [7, 12], "its": [7, 25, 29, 32, 37], "coeffici": [7, 12, 25, 26, 27, 29, 30, 31, 32, 33, 37], "precondit": 7, "have": [7, 9, 11, 12, 18, 19, 21, 29, 30, 31, 33, 37], "bold": [7, 19, 31, 33, 37], "dwi": [7, 19, 33, 37], "dataset": [7, 11, 12, 19, 25, 26, 30, 32, 33, 34], "even": [7, 11], "mprage": 7, "principl": 7, "without": [7, 9, 11, 31, 33], "gone": 7, "hmc": [7, 12], "sdc": [7, 12, 19, 23, 27, 33, 37], "matric": [7, 12, 25, 33], "account": [7, 15, 18, 37], "head": [7, 12, 25], "motion": [7, 12, 25], "resampl": [7, 11, 12, 18, 26, 31, 33], "doe": [7, 12, 15], "move": [7, 10, 12, 26, 33], "anymor": 7, "align": [7, 12, 18, 26, 33, 37], "e": [7, 9, 12, 14, 15, 18, 31, 32, 33], "g": [7, 9, 15, 31, 32, 33], "magnitud": [7, 9, 23, 26, 29, 32, 33, 37], "et": [7, 37], "al": [7, 18, 37], "refer": [7, 10, 11, 12, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34], "algorithm": [7, 33, 37], "first": [7, 11, 15, 30, 31, 33, 37], "grid": [7, 12, 18, 25, 30, 33], "project": [7, 18, 37], "onto": [7, 12, 37], "space": [7, 12, 15, 25, 26, 31, 32, 33, 37], "reconstruct": [7, 12, 15, 37], "abov": [7, 29, 35], "second": [7, 12, 15, 31, 37], "step": [7, 12, 37], "find": [7, 15, 19, 33, 37], "locat": [7, 12, 32, 37], "everi": [7, 12, 37], "voxel": [7, 12, 18, 23, 25, 31, 37], "each": [7, 12, 30], "timepoint": [7, 31], "mean": [7, 9, 19, 37], "progress": 7, "reced": 7, "along": [7, 15, 25, 33, 37], "phase": [7, 9, 12, 17, 19, 29, 30, 31, 33, 34], "encod": [7, 9, 12, 19, 30, 31, 33, 37], "axi": [7, 11, 12, 37], "coordin": [7, 11, 12, 18, 37], "With": [7, 15, 33], "those": [7, 37], "known": [7, 15], "interpol": [7, 12, 25, 33, 37], "trivial": 7, "spatial": [7, 11, 12], "new": [7, 14, 18, 34], "in_coeff": 7, "item": [7, 8, 9, 11, 14, 32], "calcul": [7, 8, 9, 12, 15, 17, 23, 25, 27, 29, 31, 33, 37], "stage": [7, 37], "in_data": [7, 8, 11, 30], "pe_dir": [7, 8, 9, 11, 12, 18], "j": [7, 8, 9, 11, 12, 15, 18, 33, 37], "k": [7, 8, 9, 11, 12, 18, 37], "direct": [7, 8, 9, 11, 15, 18, 19, 30, 31, 33, 34], "ro_tim": [7, 9, 12], "readout": [7, 8, 9, 12, 15, 25, 37], "approx": [7, 12, 15], "boolean": [7, 9, 10, 11, 32], "origin": [7, 11, 12, 32, 33], "rotat": [7, 9, 18, 33, 37], "rather": [7, 12, 33, 37], "than": [7, 33], "data2fmap_xfm": 7, "mutual": [7, 11, 37], "exclus": [7, 11, 19], "m": [7, 35, 37], "p": [7, 37], "d": [7, 11, 14, 33], "t": [7, 12, 15, 17, 37], "_": [7, 14], "x": [7, 8, 11, 21, 34], "fmap2data_xfm": 7, "in_xfm": 7, "num_thread": [7, 11, 12], "integ": [7, 11, 23, 37], "number": [7, 11, 12, 15, 18, 25, 26, 27, 29, 30, 31, 33, 37], "thread": [7, 11, 25, 26, 27, 29, 33], "out_correct": 7, "out_field": [7, 11], "approxim": [7, 12, 31, 33], "tensor": [7, 12, 33, 37], "product": [7, 12, 18, 33], "effect": [7, 15, 33, 37], "smooth": [7, 37], "remov": [7, 12, 23, 29, 33], "spike": 7, "other": [7, 12, 18, 19, 33, 34, 35], "nois": [7, 11, 29], "well": [7, 33, 37], "extrapol": [7, 12, 33], "beyond": 7, "allevi": 7, "boundari": 7, "resolv": [7, 33], "optim": [7, 33, 37], "problem": [7, 15, 33, 37], "obtain": [7, 15, 18, 37], "c": [7, 12, 14, 35], "mathbf": [7, 12], "best": 7, "sampl": [7, 12, 18], "within": [7, 15, 33, 37], "eq": [7, 12, 15, 37], "17": [7, 37], "2d": 7, "unser1999": [7, 12], "here": [7, 12, 15, 18, 37], "3d": [7, 11, 37], "formul": [7, 15], "adapt": [7, 33], "unser": 7, "perfect": 7, "signal": 7, "process": [7, 18, 25, 26, 27, 29, 34, 37], "ieee": [7, 37], "magazin": 7, "16": [7, 34, 35, 37], "6": [7, 9, 12, 29, 34, 35, 37], "22": [7, 34], "38": 7, "1999": 7, "evalu": [7, 12, 33, 37], "cubic": [7, 12], "psi": [7, 12], "bs_space": 7, "form": [7, 11, 12, 18, 33], "between": [7, 37], "control": [7, 12, 26], "point": [7, 12, 37], "40": [7, 16], "20": [7, 34, 37], "debug": [7, 25, 26, 27, 29, 30, 31, 33], "extra": [7, 32], "asset": 7, "outsid": [7, 10, 12], "in_mask": [7, 11], "mode": [7, 12, 25, 26, 29, 30, 31, 33, 37], "median": 7, "ridge_alpha": 7, "regular": [7, 12, 31], "zooms_min": 7, "legal": 7, "limit": [7, 33], "minimum": [7, 33], "zoom": [7, 18, 33, 37], "set": [7, 12, 15, 19, 25, 31, 32, 33, 35, 37], "out_coeff": 7, "out_error": 7, "out_extrapol": 7, "revis": [7, 33], "orient": [7, 18, 33], "topup": [7, 8, 11, 30, 33, 37], "fieldcoeff": [7, 33], "just": [7, 12, 23, 29], "shape": [7, 9, 12, 33], "fixat": 7, "decim": 7, "factor": [7, 11, 15, 18, 29, 37], "ad": [7, 33], "pixel": [7, 15], "dimens": [7, 11, 12], "one": [7, 9, 12, 18, 19, 29, 33, 37], "reason": [7, 33], "why": 7, "fsl": [7, 8, 15, 29, 30, 33, 35, 37], "segfault": [7, 11], "ha": [7, 12, 15, 18, 19, 33, 37], "odd": [7, 33], "more": [7, 9, 19, 29, 31, 32, 33, 37], "These": [7, 19, 35, 37], "zero": [7, 10, 19, 33], "center": [7, 15, 33], "plumb": [7, 11, 33], "cardin": [7, 33], "ax": [7, 11, 12, 18, 33, 37], "q": 7, "nifti": [7, 11, 12, 19, 32, 37], "alwai": 7, "diagon": 7, "henc": 7, "director": 7, "cosin": [7, 11, 18], "posit": [7, 11, 18, 37], "In": [7, 9, 12, 18, 37], "word": [7, 12, 18], "either": [7, 29], "ra": [7, 12, 18, 33], "asr": 7, "sar": 7, "sra": 7, "modifi": [7, 21, 33], "fledg": 7, "therefor": [7, 12, 18, 30, 37], "header": [7, 11, 32, 33], "updat": [7, 9, 12, 18, 33, 37], "becaus": [7, 15, 19, 37], "obliqu": [7, 11, 18, 33, 37], "retain": 7, "mark": 7, "code": [7, 11, 25, 26, 29, 30, 31, 33], "fmap_ref": [7, 26, 27, 29, 30, 31, 32], "y": [7, 8, 11, 21, 33], "z": [7, 8, 11, 21, 33], "patch": [7, 33], "anoth": [7, 14], "rigid": 7, "bodi": 7, "fmap_target": 7, "feed": 7, "img": [7, 15, 18], "control_zooms_mm": 7, "nifti1imag": [7, 12], "embed": [7, 12], "deal": [8, 9], "variou": [8, 9], "dictionari": [8, 9, 11, 14, 19, 25, 30, 31, 32], "kei": [8, 9, 11, 14, 19, 32, 33], "pe_dir_fsl": 8, "pe_direct": 8, "readout_tim": 8, "pe": [8, 15, 25, 30, 31, 37], "blip": [8, 33], "thei": [8, 33, 37], "fed": [8, 30, 37], "pe_dirs_fsl": 8, "convent": 8, "total": [8, 9, 12, 15, 37], "out_data": [8, 11], "hz": [9, 10, 12, 17, 25, 29, 32, 33, 37], "check": [9, 11, 33, 35], "pair": [9, 14, 19, 29, 33], "phase1": [9, 29, 33], "phase2": [9, 29], "fmap_fil": 9, "_phase1": 9, "_phase2": 9, "mag_fil": 9, "_magnitude1": 9, "_magnitude2": 9, "_phasediff": 9, "_fieldmap": [9, 29], "_magnitud": 9, "If": [9, 11, 12, 15, 19, 31, 37], "two": [9, 15, 17, 18, 19, 29, 30, 33, 37], "regist": [9, 12, 33], "them": 9, "inspect": 9, "evid": 9, "significantli": 9, "fov": [9, 33], "02rad": 9, "1mm": 9, "both": [9, 10, 18, 33, 37], "shift": [9, 12, 15, 37], "assum": [9, 31, 37], "50mm": 9, "run": [9, 11, 19, 25, 26, 29, 30, 31, 33], "mri_robust_regist": 9, "submit": [9, 33], "diff": 9, "verifi": 9, "rot_thresh": 9, "threshold": [9, 31], "radian": [9, 37], "02": 9, "trans_thresh": 9, "translat": 9, "mm": [9, 31], "convert": [9, 11, 12, 17, 29, 33, 37], "b0": [9, 34], "displac": [9, 11, 12, 25, 31, 33, 37], "demean": [9, 33], "regress": 9, "itk_transform": 9, "whether": [9, 18, 25, 29, 30, 31, 32], "itk": [9, 11, 12, 25, 26], "ant": [9, 11, 12, 26, 33, 35, 37], "u": [9, 17], "4096": 9, "rang": [9, 12, 29, 33, 37], "28": [9, 29, 33], "in_meta": [9, 11, 15, 17, 31], "in_phas": [9, 17], "phase_diff": 9, "special": [10, 14], "reportcapableinterfac": 10, "abstract": 10, "mixin": 10, "apply_mask": 10, "max_alpha": [10, 21], "maximum": [10, 12, 25, 26, 27, 29, 33], "alpha": 10, "channel": [10, 37], "7": [10, 21, 34, 37], "moving_label": 10, "label": [10, 12, 15, 19, 21, 27, 33, 37], "mosaic": 10, "out_report": 10, "visual": [10, 21, 33, 37], "report": [10, 15, 32, 33], "svg": [10, 25, 26, 29, 30, 31], "reference_label": 10, "show": [10, 33], "shown": 10, "3dqwarp": [11, 30, 33, 37], "compat": [11, 12, 33, 37], "warp": [11, 31, 37], "copyheaderinterfac": 11, "execut": [11, 12, 19, 31, 37], "copy_head": 11, "capabl": 11, "input_imag": 11, "scalar": 11, "command": [11, 35], "line": [11, 35], "save_nois": 11, "save": [11, 27, 32, 33], "noise_imag": 11, "arg": [11, 14], "addit": [11, 18, 26, 35], "forc": [11, 19, 37], "specifi": [11, 31, 33], "dimension": [11, 37], "tri": 11, "environ": [11, 35], "byte": [11, 19], "variabl": 11, "noise_model": 11, "gaussian": 11, "rician": 11, "emploi": 11, "model": [11, 37], "output_imag": 11, "version": [11, 33, 35], "o": [11, 12, 29, 32, 37], "shrink_factor": 11, "larg": [11, 33], "consum": 11, "To": [11, 19, 33, 37], "lessen": 11, "comput": [11, 12, 31], "shrink": 11, "singl": [11, 12, 19, 27, 33, 37], "describ": [11, 33, 37], "verbos": [11, 33], "v": [11, 37], "make": [11, 33, 35, 37], "potenti": [11, 33], "4d": [11, 12, 33], "max_tr": 11, "onli": [11, 12, 18, 19, 33, 37], "pick": [11, 19], "tr": 11, "50": [11, 33], "out_list": 11, "out_meta": [11, 32], "uneven": 11, "slice": [11, 33, 37], "avoid": [11, 33], "chang": [11, 19, 33], "standard": [11, 15, 33], "configur": [11, 12, 26, 30, 31], "stack": 11, "pad": [11, 18, 33], "wa": [11, 12, 29, 30, 31, 32], "reorient": [11, 18, 33], "polar": [11, 18, 33, 37], "in_orient": 11, "in_epi": [11, 31], "in_field": 11, "in_plumb": 11, "out_epi": 11, "target_orient": 11, "system": [11, 18, 35], "unwarp": [12, 25, 30, 31, 33, 34], "deform": [12, 31, 37], "caus": 12, "suscept": [12, 19, 31, 33, 34, 37], "deriv": [12, 27, 32, 33, 34, 37], "attempt": [12, 19, 37], "represent": [12, 33, 37], "independ": 12, "see": [12, 19, 33, 37], "That": 12, "achiev": 12, "multi": [12, 19, 37], "linear": [12, 37], "combin": [12, 27], "basi": [12, 37], "eqref": [12, 15, 37], "sum_": 12, "k_1": 12, "k_2": 12, "k_3": 12, "tag": [12, 15, 33, 37], "spatialimag": [12, 18, 33], "sequenc": [12, 29, 34], "xfm": [12, 18], "ndarrai": 12, "xfm_data2fmap": 12, "order": [12, 18, 21, 33], "int": [12, 16, 18, 23, 25, 26, 27, 29, 30, 31], "constant": 12, "cval": 12, "prefilt": [12, 18], "output_dtyp": 12, "dtype": [12, 32], "allow_neg": 12, "handl": [12, 33, 35], "parallel": [12, 15, 30, 31, 37], "phaseencodingdirect": [12, 15, 18, 19], "scan": [12, 15, 34, 37], "express": [12, 37], "physic": [12, 37], "realign": 12, "seri": [12, 34], "volum": [12, 30, 31, 33], "numpi": [12, 32], "target_refer": 12, "12": [12, 34], "degre": 12, "freedom": 12, "carri": 12, "target_affin": 12, "framework": [12, 33, 37], "our": [12, 19, 33], "reflect": 12, "nearest": 12, "mirror": 12, "determin": [12, 18], "how": [12, 15, 19, 35, 37], "extend": 12, "overflow": 12, "border": 12, "arrai": [12, 18, 37], "befor": [12, 33], "float64": 12, "slightli": 12, "blur": 12, "unless": [12, 33], "overrid": [12, 33], "instead": [12, 33], "propag": [12, 32], "upper": 12, "bound": 12, "memori": [12, 16, 33], "neg": 12, "introduc": [12, 37], "happen": 12, "nonneg": 12, "gt": 12, "your": [12, 35], "per": [12, 15, 19, 29, 33], "matrix": [12, 15, 33], "vsm": [12, 33, 37], "extent": [12, 18], "fourth": 12, "drop": [12, 33], "intern": [12, 30, 31], "reus": [12, 33], "itk_format": 12, "section": [12, 37], "nibabel": [12, 18], "xyz_nii": 12, "invers": [12, 18, 31], "previou": [12, 33, 37], "format": [12, 25, 37], "fmap_nii": 12, "target_nii": 12, "ctrl_nii": 12, "float32": 12, "weight": [12, 34], "s_1": 12, "s_2": 12, "s_3": 12, "knot": 12, "kernel": [12, 33], "beta": 12, "cdot": [12, 15, 37], "1d": 12, "piecewis": 12, "close": 12, "By": [12, 37], "iter": 12, "fall": 12, "compact": [12, 37], "support": [12, 29, 30, 31, 33], "out": [12, 32, 33], "dismiss": [12, 19], "lighten": 12, "final": [12, 19, 33, 34], "easili": [12, 34], "design": [12, 33, 34], "spars": 12, "async": 12, "fulldataset": 12, "fmap_hz": 12, "pe_info": 12, "max_concurr": 12, "across": [12, 30, 31, 33], "sign": 12, "must": [12, 19, 30, 35], "revers": [12, 14, 15, 37], "obj": [12, 29], "hmc_xfm": 12, "semaphor": 12, "attach": 12, "loop": 12, "bidirect": 14, "hashmap": 14, "track": 14, "file3": 14, "txt": 14, "file4": 14, "file1": 14, "file2": 14, "auto_00000": [14, 19], "auto_00002": [14, 19], "file5": 14, "get": [14, 15, 33], "particular": [14, 29], "properti": [14, 18], "dict": [14, 17, 19, 29, 30, 31, 32], "del": 14, "typeerror": 14, "self": [14, 33], "keyerror": 14, "alreadi": [14, 29, 33, 37], "unhash": 14, "val": 14, "auto_00001": [14, 19], "third": 14, "cannot": 14, "repeat": 14, "insert": [14, 33], "automat": [14, 19, 31], "manipul": [15, 17, 33], "grayscal": [15, 18], "morpholog": [15, 18], "quick": [15, 18], "t_": [15, 37], "text": [15, 17, 29, 37], "ro": [15, 37], "mechan": 15, "store": [15, 32, 37], "found": [15, 19, 33, 35, 37], "meta": 15, "05251": 15, "altern": [15, 37], "echo": [15, 29, 33, 34, 37], "ee": 15, "effectiveechospac": 15, "Then": [15, 37], "n_": 15, "rotim": 15, "00059": 15, "nonstandard": 15, "further": [15, 37], "confus": 15, "acceler": [15, 37], "grappa": 15, "arc": 15, "etc": [15, 33], "f_": 15, "acc": 15, "left": [15, 32, 33], "lfloor": 15, "frac": [15, 37], "right": [15, 16, 32], "rfloor": 15, "echospac": 15, "00119341": 15, "parallelreductionfactorinplan": 15, "philip": 15, "been": [15, 19, 33, 37], "quit": 15, "bit": 15, "engin": 15, "discuss": [15, 37], "around": [15, 18, 21, 33], "vendor": 15, "done": [15, 29, 33], "dr": 15, "rorden": 15, "summar": 15, "post": 15, "seem": 15, "wf": 15, "gamma": [15, 37], "delta_": [15, 17, 37], "w": [15, 33], "water": 15, "fat": 15, "strength": 15, "gyromagnet": [15, 37], "ratio": [15, 37], "ppm": 15, "plane": 15, "sens": 15, "absolut": [15, 18], "allow": [15, 19, 33], "train": 15, "length": 15, "size": [15, 25], "neither": 15, "acquisit": [15, 29, 34, 37], "strang": 15, "434": 15, "215": [15, 33], "earli": 15, "held": 15, "listserv": 15, "As": [15, 33, 35], "equival": [15, 29, 37], "frequenc": 15, "mhz": 15, "consol": 15, "prefer": 15, "accuraci": 15, "magnet": 15, "onc": 15, "waterfatshift": 15, "9": [15, 34, 35], "2227266": 15, "epifactor": 15, "35": 15, "imagingfrequ": 15, "127": [15, 33], "7325": 15, "5f": [15, 17], "magneticfieldstrength": 15, "enough": 15, "rais": 15, "hi": 15, "thorough": 15, "assess": 15, "matter": 15, "pravesh": 15, "parekh": 15, "wonder": 15, "review": 15, "neurostar": 15, "link": [15, 33, 37], "regard": 15, "voyag": 15, "pleas": [15, 33], "note": 15, "oe": 15, "believ": 15, "statement": 15, "about": [15, 33], "wrong": 15, "disappear": 15, "spinoza": 15, "guid": [15, 29], "preprocess": [15, 27, 29, 31, 32, 33, 34, 37], "basic": [16, 19], "miscellan": 16, "logger": [16, 19], "inlist": 16, "pop": 16, "otherwis": [16, 33], "untouch": 16, "somewher": 16, "probe": 16, "free": 16, "now": [16, 33], "newpath": 17, "arbitrari": [17, 18], "in_valu": 17, "te": [17, 29, 37], "echotime1": [17, 29], "00522": 17, "00768": 17, "00246": 17, "echotimediffer": 17, "in_refer": 18, "factor_tol": 18, "0001": 18, "cover": [18, 33], "whose": 18, "increas": [18, 33], "resolut": [18, 33], "extrem": [18, 33], "toler": [18, 33], "respect": 18, "la": 18, "source_ornt": 18, "target_ornt": 18, "natur": 18, "group": [18, 33], "ident": [18, 33], "thu": 18, "precomput": 18, "axcodes2ornt": 18, "psl": 18, "lp": 18, "air": [18, 29], "invert": 18, "ornt_transform": 18, "request": [18, 33], "anat_fil": 19, "bidsfil": 19, "layout": 19, "bidslayout": 19, "session": [19, 33, 37], "base_ent": 19, "anatom": [19, 26, 29, 31, 32, 33, 37], "pybid": [19, 33], "particip": [19, 27], "One": [19, 32, 37], "queri": [19, 33], "sbref": [19, 33], "place": 19, "diffus": [19, 37], "fmapless": [19, 37], "force_fmapless": [19, 37], "bids_filt": 19, "anat_suffix": 19, "heurist": [19, 33, 37], "less": [19, 27, 29, 30, 31, 33, 34], "_dwi": 19, "_bold": 19, "candid": [19, 37], "_t1w": 19, "complic": [19, 37], "_t2w": 19, "_sbref": 19, "manual": 19, "user": [19, 29, 33, 34], "suffic": 19, "skip": 19, "relai": 19, "messag": [19, 33], "lower": 19, "inclus": 19, "successfulli": 19, "built": [19, 37], "present": [19, 33], "ds000054": 19, "fmriprep": [19, 33], "magnitude1": [19, 33], "magnitude2": [19, 33], "100185": 19, "openneuro": 19, "four": 19, "ap": 19, "pa": [19, 33], "ds001771": [19, 33], "36": 19, "ds001600": 19, "test": [19, 33], "mani": [19, 37], "auto_00003": 19, "auto_00004": 19, "auto_00005": 19, "simplifi": [19, 33], "hcp": [19, 33], "purpos": [19, 26, 37], "hcp101006": 19, "101006": 19, "auto_00006": 19, "auto_00007": 19, "auto_00008": 19, "dsa": 19, "auto_": 19, "dsb": 19, "fm": 19, "likewis": 19, "comprehens": [19, 33], "veri": 19, "few": 19, "come": 19, "back": [19, 29, 33], "miss": [19, 33], "correctli": [19, 33], "investig": 19, "ds000206": 19, "05": [19, 34, 37], "dsc": 19, "pepolar4p": 19, "prioriti": 19, "opaque_perc": 21, "30": [21, 34], "transparent_perc": 21, "8": [21, 34], "coolwarm": 21, "color": 21, "scale": [21, 25, 29, 33], "transpar": [21, 33], "middl": 21, "anat_nii": 21, "div_id": 21, "plot_param": 21, "cut": 21, "estimate_bright": 21, "contour": 21, "compress": [21, 32], "auto": [21, 33], "overlai": 21, "overlay_param": 21, "plot": [21, 33], "foreground": [21, 33], "background": 21, "view": [21, 33], "axial": 21, "coron": 21, "sagitt": 21, "brainextraction_wf": 23, "nonbrain": 23, "tissu": 23, "bspline_dist": 23, "replac": [23, 33], "distanc": [23, 33], "separ": [23, 29, 33], "n4": [23, 29, 33], "smart": 23, "clip": [23, 37], "out_brain": 23, "probabl": 23, "random": 23, "walker": 23, "reach": 23, "soft": 23, "free_mem": 25, "omp_nthread": [25, 26, 27, 29, 30, 31], "unwarp_wf": [25, 33], "graph": [25, 26, 29, 30, 31], "png": [25, 26, 29, 30, 31], "pdf": [25, 26, 29, 30, 31], "individu": [25, 26, 27, 29, 37], "sloppi": [25, 26, 27, 29, 30, 31, 33], "fmap_coeff": [25, 26, 27, 29, 30, 31, 32], "hmc_xform": 25, "inhomogen": [25, 37], "fieldwarp": [25, 33], "appropri": [25, 33], "corrected_mask": 25, "fast": [25, 26, 29, 30, 31, 33, 37], "thereof": 26, "write_coeff": [26, 32], "coeff2epi_wf": 26, "trace": 26, "target_ref": 26, "target_mask": 26, "skull": [26, 29, 31, 37], "strip": [26, 29, 31, 37], "fmap_mask": [26, 29, 30, 32], "qualiti": 26, "target2fmap_xfm": 26, "style": 26, "produc": [26, 37], "antsapplytransform": [26, 37], "latter": 26, "output_dir": [27, 32], "fmap_preproc_wf": 27, "faster": 27, "precis": 27, "in_": 27, "depend": [27, 33, 34], "out_": 27, "measur": 29, "fmap_wf": 29, "mri": [29, 34, 37], "need": [29, 33], "surround": 29, "region": [29, 31, 37], "accur": [29, 30, 31, 33, 37], "short": [29, 30, 31], "descript": [29, 30, 31, 33, 35], "magnitude_wf": 29, "prepar": [29, 31, 33, 37], "part": [29, 34], "averag": [29, 31, 33, 37], "b1": 29, "nonuniform": 29, "phdiff_wf": 29, "consecut": 29, "besid": 29, "subtract": [29, 33], "core": 29, "reli": 29, "unwrap": [29, 33, 37], "prelud": 29, "jenkinson2003": [29, 37], "take": [29, 30, 37], "pi": [29, 37], "dotsb": [29, 37], "massag": [29, 33], "delta": [29, 37], "elsewher": 29, "subsequ": [29, 37], "pepolar_estimate_wf": 30, "afni": [30, 35, 37], "oppos": 30, "orthogon": 30, "task": [30, 31], "cpu": [30, 31, 33], "taken": 30, "convers": [30, 31, 33], "grid_refer": 30, "syn_preprocessing_wf": 31, "auto_bold_nss": 31, "t1w_invers": 31, "co": [31, 37], "nonsteadi": 31, "state": [31, 34], "detect": [31, 33], "intens": [31, 33, 37], "look": 31, "t2": 31, "merg": [31, 33], "togeth": [31, 33], "t_mask": 31, "Not": 31, "in_anat": 31, "t2w": [31, 33, 37], "mask_anat": 31, "std2anat_xfm": 31, "mni": 31, "templat": 31, "epi_ref": 31, "anat_ref": 31, "anat_mask": 31, "sd_prior": 31, "area": 31, "strong": 31, "sd": [31, 37], "cost": [31, 37], "atlas_threshold": 31, "syn_sdc_wf": 31, "restrict": [31, 33], "anterior": 31, "posterior": 31, "3mm": 31, "atla": [31, 33], "exclud": 31, "metric": 31, "below": [31, 37], "out_warp": [31, 33], "ref_mask": 31, "img_mask": 31, "histogram": [31, 37], "write": [32, 33], "allowed_ent": 32, "overload": 32, "source_fil": 32, "base_directori": 32, "check_hdr": 32, "fix": [32, 33, 37], "uncompress": 32, "unmodifi": 32, "data_dtyp": 32, "datatyp": 32, "coerc": 32, "tomatch": 32, "dismiss_ent": 32, "meta_dict": 32, "fixed_hdr": 32, "bids_fmap_id": 32, "custom_ent": 32, "fmap_derivatives_wf": 32, "datasink": 32, "defin": [32, 37], "written": [32, 35], "serv": 32, "fmap_typ": 32, "fmap_reports_wf": 32, "batteri": 32, "bug": 33, "lsqr": 33, "solver": 33, "rerun": 33, "366": 33, "367": 33, "rf": 33, "priorit": 33, "shortest": 33, "364": 33, "featur": 33, "behavior": 33, "addition": 33, "share": 33, "small": 33, "ux": 33, "themselv": 33, "360": 33, "enh": 33, "split": 33, "312": 33, "non": [33, 37], "358": 33, "355": 33, "356": 33, "intent": [33, 37], "342": 33, "ci": 33, "codecov": 33, "upload": 33, "348": 33, "inconsist": 33, "treatment": 33, "scanner": [33, 37], "were": [33, 37], "impact": 33, "354": 33, "captur": 33, "partial": 33, "351": 33, "incomplet": 33, "log": 33, "341": 33, "failur": 33, "343": 33, "nibabi": 33, "339": 33, "overli": 33, "335": 33, "334": 33, "squeez": 33, "simplebeforeaft": 33, "337": 33, "maint": 33, "circleci": 33, "secret": 33, "setup": 33, "org": 33, "329": 33, "326": 33, "switch": 33, "miniconda": 33, "instal": [33, 34], "conda": 33, "322": 33, "affect": 33, "324": 33, "doc": 33, "notebook": 33, "285": 33, "dynam": 33, "particularli": 33, "node": 33, "choos": 33, "constraint": 33, "321": 33, "thank": 33, "basil": 33, "pinsard": 33, "contribut": 33, "start": 33, "collat": 33, "317": 33, "319": 33, "coloc": 33, "308": 33, "scipi": 33, "311": 33, "pacifi": 33, "deprec": 33, "warn": 33, "stat": 33, "309": 33, "303": 33, "dens": 33, "wai": 33, "299": 33, "alter": 33, "basenam": 33, "293": 33, "287": 33, "288": 33, "coeff2epi": 33, "relat": 33, "278": 33, "4mm": 33, "re": 33, "314": 33, "n_proc": 33, "315": 33, "298": 33, "dure": 33, "292": 33, "304": 33, "integr": [33, 37], "downsampl": 33, "high": [33, 37], "301": 33, "284": 33, "usabl": 33, "257": 33, "robust": [33, 34, 37], "280": 33, "housekeep": 33, "302": 33, "gh": 33, "action": 33, "latest": 33, "282": 33, "keep": 33, "date": 33, "281": 33, "unavil": 33, "osf": 33, "remot": 33, "datalad": 33, "277": 33, "unus": 33, "276": 33, "concurr": 33, "permiss": 33, "313": 33, "roll": 33, "unittest": 33, "runner": 33, "ubuntu": 33, "310": 33, "trigger": 33, "weekli": 33, "270": 33, "incorpor": 33, "relax": 33, "concaten": 33, "265": 33, "minor": 33, "newest": 33, "niworkflow": 33, "distinct": 33, "261": 33, "mass": 33, "253": 33, "loosen": 33, "269": 33, "issu": 33, "21": 33, "next": 33, "262": 33, "intersphinx": 33, "url": 33, "263": 33, "258": 33, "docker": 33, "254": 33, "boilerpl": 33, "229": 33, "ishandl": 33, "higher": [33, 37], "251": 33, "b0field": 33, "bring": 33, "detail": [33, 37], "248": 33, "b0fieldsourc": 33, "247": 33, "deep": 33, "toward": 33, "overhaul": 33, "239": 33, "host": 33, "multivers": 33, "243": 33, "niprep": [33, 34], "240": [33, 37], "bugfix": 33, "discov": [33, 34], "237": 33, "228": 33, "234": 33, "page": 33, "push": 33, "histori": 33, "230": 33, "address": 33, "217": [33, 37], "expos": 33, "224": 33, "openpgp": 33, "sk": 33, "keyserv": 33, "223": 33, "hotfix": 33, "enhanc": [33, 37], "fine": 33, "tune": 33, "upstream": 33, "intensityclip": 33, "216": 33, "robustaverag": 33, "214": 33, "copyright": 33, "notic": 33, "comment": 33, "apach": 33, "212": 33, "uniform": [33, 37], "197": [33, 37], "210": 33, "209": 33, "hot": 33, "relev": 33, "inted": 33, "reliabl": 33, "api": [33, 34, 37], "advanc": 33, "nitranform": 33, "evad": 33, "fiddl": 33, "sure": [33, 35], "207": 33, "normal": [33, 37], "202": 33, "199": 33, "renam": 33, "182": 33, "180": 33, "204": 33, "191": 33, "188": 33, "pipelin": [33, 37], "184": 33, "rodent": 33, "inu": 33, "178": [33, 37], "adopt": 33, "176": 33, "typo": 33, "codespel": 33, "205": 33, "doubl": 33, "200": 33, "divid": [33, 37], "ambigu": 33, "smaller": 33, "focus": 33, "190": 33, "github": 33, "upgrad": 33, "185": 33, "minim": [33, 34], "major": [33, 37], "softwar": [33, 35, 37], "vision": 33, "subordin": 33, "inlin": 33, "smriprep": 33, "idea": 33, "consid": 33, "citizen": 33, "vein": 33, "ey": 33, "suffici": 33, "under": 33, "suit": [33, 37], "dmriprep": 33, "exercis": 33, "artifact": [33, 37], "popul": 33, "piec": 33, "forward": 33, "leverag": 33, "choic": 33, "boldref": 33, "accordingli": 33, "coverag": 33, "cleanup": 33, "promin": [33, 37], "pull": 33, "conduc": 33, "bet": 33, "174": 33, "svgutil": 33, "break": 33, "175": 33, "misconfigur": 33, "170": 33, "annoi": 33, "isol": 33, "dot": 33, "168": 33, "afterward": 33, "165": 33, "sei": [33, 37], "stabil": 33, "128": 33, "166": 33, "164": 33, "simpl": 33, "161": 33, "159": 33, "157": 33, "blocksiz": 33, "156": 33, "154": 33, "simplist": 33, "152": 33, "151": 33, "fmapid": 33, "150": 33, "multiplex": 33, "outputnod": 33, "149": 33, "put": 33, "143": 33, "autogener": 33, "142": 33, "132": 33, "130": 33, "114": 33, "120": 33, "115": 33, "liter": 33, "162": 33, "155": 33, "sphinx": 33, "extens": 33, "render": 33, "131": 33, "makefil": 33, "173": 33, "retouch": 33, "sever": [33, 37], "172": 33, "160": 33, "git": 33, "archiv": 33, "protocol": [33, 34, 37], "setuptool": 33, "scm": 33, "153": 33, "migrat": 33, "travisci": 33, "complet": 33, "138": 33, "137": 33, "refactor": 33, "133": 33, "circl": 33, "122": 33, "96": 33, "flirt": 33, "config": 33, "116": 33, "repo": 33, "contributor": 33, "guidelin": 33, "anyon": 33, "develop": [33, 34, 37], "manuscript": 33, "markiewicz": 33, "christoph": 33, "goncalv": 33, "mathia": 33, "macnicol": 33, "eilidh": 33, "adebimp": 33, "azeez": 33, "blair": 33, "ross": 33, "cieslak": 33, "matthew": 33, "naveau": 33, "mika\u00ebl": 33, "sitek": 33, "kevin": 33, "r": [33, 37], "sneve": 33, "marku": 33, "h": [33, 37], "gorgolewski": 33, "krzysztof": 33, "satterthwait": 33, "theodor": 33, "poldrack": 33, "russel": 33, "esteban": [33, 37], "oscar": 33, "affili": 33, "depart": 33, "psychologi": 33, "stanford": 33, "univers": 33, "neuroimag": [33, 34, 35, 37], "king": 33, "colleg": 33, "london": 33, "perelman": 33, "school": 33, "medicin": 33, "pennsylvania": 33, "usa": 33, "cyceron": 33, "um": 33, "3408": 33, "cnr": 33, "ucbn": 33, "franc": 33, "speech": 33, "hear": 33, "bioscienc": 33, "technologi": 33, "harvard": 33, "lifespan": 33, "cognit": 33, "oslo": 33, "dept": 33, "radiologi": 33, "lausann": 33, "hospit": 33, "371": 33, "machin": 33, "branch": 33, "327": 33, "nan": 33, "104": 33, "108": 33, "newli": 33, "refacor": 33, "102": 33, "enforc": 33, "dseg": 33, "wm": 33, "select": 33, "100": 33, "98": 33, "amic": 33, "downstream": 33, "setuptools_scm": 33, "97": 33, "flexibil": 33, "95": 33, "caclul": 33, "2pi": 33, "88": 33, "mnt": 33, "90": 33, "deploy": 33, "91": 33, "nomin": 33, "central": 33, "outlier": 33, "89": 33, "connect": 33, "whenev": 33, "82": 33, "skim": 33, "80": 33, "prevent": 33, "collis": 33, "pin": 33, "449c2c2": 33, "intramodalmerg": 33, "choke": 33, "79": 33, "2e6faa0": 33, "717a69": 33, "361cd67": 33, "flexibli": 33, "cheapli": 33, "75": 33, "70": 33, "stabl": 33, "detach": 33, "off": 33, "hard": 33, "wire": 33, "mni152nlin2009casym": 33, "63": 33, "60": 33, "get_data": 33, "get_fdata": 33, "58": 33, "flow": 33, "homogen": 33, "56": 33, "57": 33, "stop": 33, "siemens2rad": 33, "old": 33, "orchestr": 33, "55": 33, "53": 33, "dedupl": 33, "postprocess": 33, "52": [33, 37], "legaci": [33, 37], "51": 33, "61": 33, "49": [33, 37], "43": 33, "fork": 33, "48": 33, "refresh": 33, "workdir": 33, "commit": 33, "47": 33, "local": 33, "45": 33, "flake8": 33, "44": 33, "distortedref": 33, "41": 33, "niflow": 33, "nipype1": 33, "39": 33, "mainten": 33, "0rc1": 33, "bad": 33, "NOT": 33, "fixup": 33, "deploi": [33, 35], "infrastructur": 33, "manifest": 33, "effigi": 33, "work": 33, "v1": 33, "librari": 34, "displai": 34, "acquir": [34, 37], "planar": [34, 37], "mr": [34, 37], "scheme": [34, 37], "art": 34, "open": 34, "being": 34, "analysi": [34, 37], "reproduc": 34, "platform": 34, "offer": 34, "extern": 34, "theori": 34, "techniqu": 34, "unsupport": 34, "implicit": 34, "t1": 34, "applic": [34, 37], "what": 34, "june": 34, "08": [34, 37], "2023": 34, "april": 34, "24": 34, "march": 34, "10": [34, 37], "januari": 34, "04": 34, "decemb": 34, "2022": 34, "09": 34, "august": 34, "29": 34, "26": 34, "13": 34, "februari": 34, "11": [34, 37], "2021": 34, "novemb": 34, "octob": 34, "15": 34, "septemb": 34, "18": 34, "14": 34, "25": 34, "juli": 34, "07": [34, 35], "2020": 34, "pre": [34, 37], "releas": 34, "27": 34, "2019": 34, "23": 34, "dockerfil": 35, "freesurf": 35, "licens": 35, "pip": 35, "habitu": 35, "__version__": 35, "pypi": 35, "neurodock": 35, "debian": 35, "behind": 37, "literatur": 37, "jezzard1995": 37, "hutton2002": 37, "summari": 37, "fig": 37, "freeli": 37, "three": 37, "proport": 37, "nutshel": 37, "suffer": 37, "proton": 37, "42": 37, "576": 37, "variat": 37, "tesla": 37, "let": 37, "veloc": 37, "s_": 37, "nonzero": 37, "compon": 37, "d_": 37, "drift": 37, "least": 37, "via": 37, "theta": 37, "elaps": 37, "simplic": 37, "fact": 37, "theta_i": 37, "offset": 37, "continu": 37, "neighbor": 37, "exploit": 37, "symmetri": 37, "andersson2003": 37, "cox1997": 37, "studi": 37, "especi": 37, "absenc": 37, "research": 37, "resort": 37, "nonlinear": 37, "propos": 37, "studholme2000": 37, "experiment": 37, "procedur": 37, "symmetr": 37, "treiber2016": 37, "huntenburg2014": 37, "wang2017": 37, "Such": 37, "aid": 37, "matt": 37, "laplacian": 37, "gradient": 37, "folder": 37, "outcom": 37, "scrutin": 37, "caution": 37, "feedback": 37, "enthusiast": 37, "There": 37, "spread": 37, "zaitsev2004": 37, "surfac": 37, "esteban2016": 37, "cornerston": 37, "plausibli": 37, "fewer": 37, "eas": 37, "try": 37, "workabl": 37, "shim": 37, "jezzard": 37, "balaban": 37, "1995": 37, "geometr": 37, "magn": 37, "reson": 37, "med": 37, "34": 37, "65": 37, "73": 37, "doi": 37, "1002": 37, "mrm": 37, "1910340111": 37, "hutton": 37, "2002": 37, "fmri": 37, "quantit": 37, "1006": 37, "nimg": 37, "2001": 37, "1054": 37, "jenkinson": 37, "2003": 37, "193": 37, "10354": 37, "andersson": 37, "spin": 37, "870": 37, "888": 37, "1016": 37, "s1053": 37, "8119": 37, "03": 37, "00336": 37, "cox": 37, "1997": 37, "nmr": 37, "biom": 37, "171": 37, "sici": 37, "1099": 37, "1492": 37, "199706": 37, "3c171": 37, "nbm453": 37, "3e3": 37, "l": 37, "studholm": 37, "2000": 37, "tran": 37, "19": 37, "1115": 37, "1127": 37, "1109": 37, "896788": 37, "treiber": 37, "2016": 37, "character": 37, "814": 37, "plo": 37, "ONE": 37, "e0152472": 37, "1371": 37, "journal": 37, "pone": 37, "0152472": 37, "wang": 37, "2017": 37, "neuroinform": 37, "3389": 37, "fninf": 37, "00017": 37, "huntenburg": 37, "2014": 37, "coregistr": 37, "berlin": 37, "master": 37, "thesi": 37, "freie": 37, "universit\u00e4t": 37, "zaitsev": 37, "2004": 37, "1156": 37, "1166": 37, "20261": 37, "driven": 37, "139": 37, "450": 37, "461": 37, "011": 37}, "objects": {"sdcflows": [[1, 0, 0, "-", "cli"], [3, 0, 0, "-", "data"], [4, 0, 0, "-", "fieldmaps"], [5, 0, 0, "-", "interfaces"], [12, 0, 0, "-", "transform"], [13, 0, 0, "-", "utils"], [20, 0, 0, "-", "viz"], [22, 0, 0, "-", "workflows"]], "sdcflows.cli": [[2, 0, 0, "-", "find_estimators"]], "sdcflows.cli.find_estimators": [[2, 1, 1, "", "gen_layout"], [2, 1, 1, "", "main"]], "sdcflows.data": [[3, 2, 1, "", "Loader"], [3, 1, 1, "", "load"]], "sdcflows.data.Loader": [[3, 3, 1, "", "as_path"], [3, 3, 1, "", "cached"], [3, 3, 1, "", "readable"]], "sdcflows.data.load": [[3, 3, 1, "", "as_path"], [3, 3, 1, "", "cached"], [3, 3, 1, "", "readable"]], "sdcflows.fieldmaps": [[4, 2, 1, "", "EstimatorType"], [4, 2, 1, "", "FieldmapEstimation"], [4, 2, 1, "", "FieldmapFile"], [4, 5, 1, "", "MetadataError"], [4, 1, 1, "", "clear_registry"], [4, 1, 1, "", "get_identifier"]], "sdcflows.fieldmaps.EstimatorType": [[4, 4, 1, "", "ANAT"], [4, 4, 1, "", "MAPPED"], [4, 4, 1, "", "PEPOLAR"], [4, 4, 1, "", "PHASEDIFF"], [4, 4, 1, "", "UNKNOWN"]], "sdcflows.fieldmaps.FieldmapEstimation": [[4, 4, 1, "", "bids_id"], [4, 3, 1, "", "get_workflow"], [4, 4, 1, "", "method"], [4, 3, 1, "", "paths"], [4, 4, 1, "", "sources"]], "sdcflows.fieldmaps.FieldmapFile": [[4, 4, 1, "", "bids_root"], [4, 3, 1, "", "check_path"], [4, 4, 1, "", "entities"], [4, 4, 1, "", "find_meta"], [4, 4, 1, "", "metadata"], [4, 4, 1, "", "path"], [4, 4, 1, "", "suffix"]], "sdcflows.interfaces": [[6, 0, 0, "-", "brainmask"], [7, 0, 0, "-", "bspline"], [8, 0, 0, "-", "epi"], [9, 0, 0, "-", "fmap"], [10, 0, 0, "-", "reportlets"], [11, 0, 0, "-", "utils"]], "sdcflows.interfaces.brainmask": [[6, 2, 1, "", "BinaryDilation"], [6, 2, 1, "", "BrainExtraction"], [6, 2, 1, "", "Union"]], "sdcflows.interfaces.bspline": [[7, 2, 1, "", "ApplyCoeffsField"], [7, 2, 1, "", "BSplineApprox"], [7, 2, 1, "", "TOPUPCoeffReorient"], [7, 2, 1, "", "TransformCoefficients"], [7, 1, 1, "", "bspline_grid"]], "sdcflows.interfaces.epi": [[8, 2, 1, "", "GetReadoutTime"], [8, 2, 1, "", "SortPEBlips"]], "sdcflows.interfaces.fmap": [[9, 2, 1, "", "CheckB0Units"], [9, 2, 1, "", "CheckRegister"], [9, 2, 1, "", "DisplacementsField2Fieldmap"], [9, 2, 1, "", "PhaseMap2rads"], [9, 2, 1, "", "Phasediff2Fieldmap"], [9, 2, 1, "", "SubtractPhases"]], "sdcflows.interfaces.reportlets": [[10, 2, 1, "", "FieldmapReportlet"]], "sdcflows.interfaces.utils": [[11, 2, 1, "", "ConvertWarp"], [11, 2, 1, "", "DenoiseImage"], [11, 2, 1, "", "Deoblique"], [11, 2, 1, "", "Flatten"], [11, 2, 1, "", "PadSlices"], [11, 2, 1, "", "PositiveDirectionCosines"], [11, 2, 1, "", "Reoblique"], [11, 2, 1, "", "ReorientImageAndMetadata"], [11, 2, 1, "", "UniformGrid"]], "sdcflows.transform": [[12, 2, 1, "", "B0FieldTransform"], [12, 1, 1, "", "disp_to_fmap"], [12, 1, 1, "", "fmap_to_disp"], [12, 1, 1, "", "grid_bspline_weights"], [12, 1, 1, "", "unwarp_parallel"], [12, 1, 1, "", "worker"]], "sdcflows.transform.B0FieldTransform": [[12, 3, 1, "", "apply"], [12, 4, 1, "", "coeffs"], [12, 3, 1, "", "fit"], [12, 4, 1, "", "mapped"], [12, 3, 1, "", "to_displacements"]], "sdcflows.utils": [[14, 0, 0, "-", "bimap"], [15, 0, 0, "-", "epimanip"], [16, 0, 0, "-", "misc"], [17, 0, 0, "-", "phasemanip"], [18, 0, 0, "-", "tools"], [19, 0, 0, "-", "wrangler"]], "sdcflows.utils.bimap": [[14, 2, 1, "", "EstimatorRegistry"], [14, 2, 1, "", "bidict"]], "sdcflows.utils.bimap.EstimatorRegistry": [[14, 3, 1, "", "get_key"], [14, 6, 1, "", "sources"]], "sdcflows.utils.bimap.bidict": [[14, 3, 1, "", "add"], [14, 3, 1, "", "clear"]], "sdcflows.utils.epimanip": [[15, 1, 1, "", "epi_mask"], [15, 1, 1, "", "get_trt"]], "sdcflows.utils.misc": [[16, 1, 1, "", "create_logger"], [16, 1, 1, "", "front"], [16, 1, 1, "", "get_free_mem"], [16, 1, 1, "", "last"]], "sdcflows.utils.phasemanip": [[17, 1, 1, "", "au2rads"], [17, 1, 1, "", "delta_te"], [17, 1, 1, "", "phdiff2fmap"], [17, 1, 1, "", "subtract_phases"]], "sdcflows.utils.tools": [[18, 1, 1, "", "brain_masker"], [18, 1, 1, "", "deoblique_and_zooms"], [18, 1, 1, "", "ensure_positive_cosines"], [18, 1, 1, "", "reorient_pedir"], [18, 1, 1, "", "resample_to_zooms"]], "sdcflows.utils.wrangler": [[19, 1, 1, "", "find_anatomical_estimators"], [19, 1, 1, "", "find_estimators"]], "sdcflows.viz": [[21, 0, 0, "-", "utils"]], "sdcflows.viz.utils": [[21, 1, 1, "", "coolwarm_transparent"], [21, 1, 1, "", "plot_registration"]], "sdcflows.workflows": [[23, 0, 0, "-", "ancillary"], [24, 0, 0, "-", "apply"], [27, 0, 0, "-", "base"], [28, 0, 0, "-", "fit"], [32, 0, 0, "-", "outputs"]], "sdcflows.workflows.ancillary": [[23, 1, 1, "", "init_brainextraction_wf"]], "sdcflows.workflows.apply": [[25, 0, 0, "-", "correction"], [26, 0, 0, "-", "registration"]], "sdcflows.workflows.apply.correction": [[25, 1, 1, "", "init_unwarp_wf"]], "sdcflows.workflows.apply.registration": [[26, 1, 1, "", "init_coeff2epi_wf"]], "sdcflows.workflows.base": [[27, 1, 1, "", "init_fmap_preproc_wf"]], "sdcflows.workflows.fit": [[29, 0, 0, "-", "fieldmap"], [30, 0, 0, "-", "pepolar"], [31, 0, 0, "-", "syn"]], "sdcflows.workflows.fit.fieldmap": [[29, 1, 1, "", "init_fmap_wf"], [29, 1, 1, "", "init_magnitude_wf"], [29, 1, 1, "", "init_phdiff_wf"]], "sdcflows.workflows.fit.pepolar": [[30, 1, 1, "", "init_3dQwarp_wf"], [30, 1, 1, "", "init_topup_wf"]], "sdcflows.workflows.fit.syn": [[31, 1, 1, "", "init_syn_preprocessing_wf"], [31, 1, 1, "", "init_syn_sdc_wf"], [31, 1, 1, "", "match_histogram"]], "sdcflows.workflows.outputs": [[32, 2, 1, "", "DerivativesDataSink"], [32, 1, 1, "", "init_fmap_derivatives_wf"], [32, 1, 1, "", "init_fmap_reports_wf"]], "sdcflows.workflows.outputs.DerivativesDataSink": [[32, 4, 1, "", "out_path_base"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method", "4": "py:attribute", "5": "py:exception", "6": "py:property"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "exception", "Python exception"], "6": ["py", "property", "Python property"]}, "titleterms": {"librari": 0, "api": 0, "applic": 0, "program": 0, "interfac": [0, 5, 6, 7, 8, 9, 10, 11], "sdcflow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], "cli": [1, 2], "packag": [1, 3, 5, 13, 20, 22, 24, 28], "submodul": [1, 5, 13, 20, 22, 24, 28], "find_estim": 2, "modul": [2, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 29, 30, 31, 32], "data": [3, 37], "fieldmap": [4, 29, 37], "brainmask": 6, "bspline": 7, "epi": 8, "fmap": 9, "reportlet": 10, "util": [11, 13, 14, 15, 16, 17, 18, 19, 21], "transform": 12, "bimap": 14, "epimanip": 15, "thank": 15, "see": 15, "also": 15, "misc": 16, "phasemanip": 17, "tool": [18, 37], "wrangler": 19, "viz": [20, 21], "workflow": [22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "subpackag": 22, "ancillari": 23, "appli": [24, 25, 26], "correct": 25, "registr": [26, 37], "base": [27, 33], "fit": [28, 29, 30, 31], "pepolar": [30, 37], "syn": 31, "output": 32, "what": 33, "": 33, "new": 33, "2": 33, "5": 33, "1": 33, "june": 33, "08": 33, "2023": 33, "0": 33, "01": 33, "4": 33, "3": 33, "april": 33, "24": 33, "20": 33, "march": 33, "10": 33, "januari": 33, "04": 33, "decemb": 33, "12": 33, "2022": 33, "09": 33, "august": 33, "29": 33, "mai": 33, "26": 33, "13": 33, "februari": 33, "11": 33, "22": 33, "2021": 33, "9": 33, "novemb": 33, "16": 33, "8": 33, "octob": 33, "15": 33, "7": 33, "septemb": 33, "30": 33, "6": 33, "18": 33, "14": 33, "05": 33, "25": 33, "author": 33, "list": 33, "paper": 33, "x": 33, "seri": 33, "juli": 33, "07": 33, "2020": 33, "pre": 33, "releas": 33, "27": 33, "2019": 33, "23": 33, "content": 34, "instal": 35, "extern": 35, "depend": 35, "method": 37, "implement": 37, "bid": 37, "specif": 37, "estim": 37, "theori": 37, "direct": 37, "b0": 37, "map": 37, "sequenc": 37, "phase": 37, "differ": 37, "techniqu": 37, "less": 37, "approach": 37, "other": 37, "unsupport": 37, "unwarp": 37, "distort": 37, "discov": 37, "dataset": 37, "explicit": 37, "b0fieldidentifi": 37, "implicit": 37, "intendedfor": 37, "t1": 37, "weight": 37, "imag": 37, "refer": 37}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Library API (application program interface)": [[0, "library-api-application-program-interface"]], "sdcflows.cli package": [[1, "sdcflows-cli-package"]], "Submodules": [[1, "submodules"], [5, "submodules"], [13, "submodules"], [20, "submodules"], [22, "submodules"], [24, "submodules"], [28, "submodules"]], "sdcflows.cli.find_estimators module": [[2, "sdcflows-cli-find-estimators-module"]], "sdcflows.data package": [[3, "sdcflows-data-package"]], "sdcflows.fieldmaps module": [[4, "sdcflows-fieldmaps-module"]], "sdcflows.interfaces package": [[5, "sdcflows-interfaces-package"]], "sdcflows.interfaces.brainmask module": [[6, "sdcflows-interfaces-brainmask-module"]], "sdcflows.interfaces.bspline module": [[7, "sdcflows-interfaces-bspline-module"]], "sdcflows.interfaces.epi module": [[8, "sdcflows-interfaces-epi-module"]], "sdcflows.interfaces.fmap module": [[9, "sdcflows-interfaces-fmap-module"]], "sdcflows.interfaces.reportlets module": [[10, "sdcflows-interfaces-reportlets-module"]], "sdcflows.interfaces.utils module": [[11, "sdcflows-interfaces-utils-module"]], "sdcflows.transform module": [[12, "sdcflows-transform-module"]], "sdcflows.utils package": [[13, "sdcflows-utils-package"]], "sdcflows.utils.bimap module": [[14, "sdcflows-utils-bimap-module"]], "sdcflows.utils.epimanip module": [[15, "sdcflows-utils-epimanip-module"]], "Thanks": [[15, null]], "See Also": [[15, null]], "sdcflows.utils.misc module": [[16, "sdcflows-utils-misc-module"]], "sdcflows.utils.phasemanip module": [[17, "sdcflows-utils-phasemanip-module"]], "sdcflows.utils.tools module": [[18, "sdcflows-utils-tools-module"]], "sdcflows.utils.wrangler module": [[19, "sdcflows-utils-wrangler-module"]], "sdcflows.viz package": [[20, "sdcflows-viz-package"]], "sdcflows.viz.utils module": [[21, "sdcflows-viz-utils-module"]], "sdcflows.workflows package": [[22, "sdcflows-workflows-package"]], "Subpackages": [[22, "subpackages"]], "sdcflows.workflows.ancillary module": [[23, "sdcflows-workflows-ancillary-module"]], "sdcflows.workflows.apply package": [[24, "sdcflows-workflows-apply-package"]], "sdcflows.workflows.apply.correction module": [[25, "sdcflows-workflows-apply-correction-module"]], "sdcflows.workflows.apply.registration module": [[26, "sdcflows-workflows-apply-registration-module"]], "sdcflows.workflows.base module": [[27, "sdcflows-workflows-base-module"]], "sdcflows.workflows.fit package": [[28, "sdcflows-workflows-fit-package"]], "sdcflows.workflows.fit.fieldmap module": [[29, "sdcflows-workflows-fit-fieldmap-module"]], "sdcflows.workflows.fit.pepolar module": [[30, "sdcflows-workflows-fit-pepolar-module"]], "sdcflows.workflows.fit.syn module": [[31, "sdcflows-workflows-fit-syn-module"]], "sdcflows.workflows.outputs module": [[32, "sdcflows-workflows-outputs-module"]], "What\u2019s new?": [[33, "what-s-new"]], "2.5.1 (June 08, 2023)": [[33, "june-08-2023"]], "2.5.0 (June 01, 2023)": [[33, "june-01-2023"]], "2.4.3 (April 24, 2023)": [[33, "april-24-2023"]], "2.4.2 (April 20, 2023)": [[33, "april-20-2023"]], "2.4.1 (March 20, 2023)": [[33, "march-20-2023"]], "2.4.0 (March 10, 2023)": [[33, "march-10-2023"]], "2.3.0 (March 01, 2023)": [[33, "march-01-2023"]], "2.2.2 (January 04, 2023)": [[33, "january-04-2023"]], "2.2.1 (December 12, 2022)": [[33, "december-12-2022"]], "2.2.0 (December 09, 2022)": [[33, "december-09-2022"]], "2.1.1 (August 29, 2022)": [[33, "august-29-2022"]], "2.1.0 (May 26, 2022)": [[33, "may-26-2022"]], "2.0.13 (April 08, 2022)": [[33, "april-08-2022"]], "2.0.12 (February 08, 2022)": [[33, "february-08-2022"]], "2.0.11 (January 22, 2022)": [[33, "january-22-2022"]], "2.0.10 (December 13, 2021)": [[33, "december-13-2021"]], "2.0.9 (November 16, 2021)": [[33, "november-16-2021"]], "2.0.8 (October 15, 2021)": [[33, "october-15-2021"]], "2.0.7 (September 30, 2021)": [[33, "september-30-2021"]], "2.0.6 (September 1, 2021)": [[33, "september-1-2021"]], "2.0.5 (August 24, 2021)": [[33, "august-24-2021"]], "2.0.4 (May 18, 2021)": [[33, "may-18-2021"]], "2.0.3 (May 14, 2021)": [[33, "may-14-2021"]], "2.0.2 (May 11, 2021)": [[33, "may-11-2021"]], "2.0.1 (March 05, 2021)": [[33, "march-05-2021"]], "2.0.0 (January 25, 2021)": [[33, "january-25-2021"]], "Author list for papers based on SDCFlows 2.0.x series": [[33, null]], "1.3.x series": [[33, "x-series"]], "1.3.4 (July 07, 2023)": [[33, "july-07-2023"]], "1.3.3 (September 4, 2020)": [[33, "september-4-2020"]], "1.3.2 (August 14, 2020)": [[33, "august-14-2020"]], "1.3.1 (May 22, 2020)": [[33, "may-22-2020"]], "1.3.0 (May 4, 2020)": [[33, "may-4-2020"]], "Pre-1.3.x releases": [[33, "pre-1-3-x-releases"]], "1.2.2 (April 16, 2020)": [[33, "april-16-2020"]], "1.2.1 (April 01, 2020)": [[33, "april-01-2020"]], "1.2.0 (February 15, 2020)": [[33, "february-15-2020"]], "1.1.0 (February 3, 2020)": [[33, "february-3-2020"]], "1.0.6 (April 15, 2020)": [[33, "april-15-2020"]], "1.0.5 (February 14, 2020)": [[33, "february-14-2020"]], "1.0.4 (January 27, 2020)": [[33, "january-27-2020"]], "1.0.3 (December 18, 2019)": [[33, "december-18-2019"]], "1.0.2 (December 18, 2019)": [[33, "id1"]], "1.0.1 (December 04, 2019)": [[33, "december-04-2019"]], "1.0.0 (November 25, 2019)": [[33, "november-25-2019"]], "0.1.4 (November 22, 2019)": [[33, "november-22-2019"]], "0.1.3 (October 15, 2019)": [[33, "october-15-2019"]], "0.1.2 (October 10, 2019)": [[33, "october-10-2019"]], "0.1.1 (July 23, 2019)": [[33, "july-23-2019"]], "0.1.0 (July 22, 2019)": [[33, "july-22-2019"]], "SDCFlows": [[34, "sdcflows"]], "Contents": [[34, "contents"]], "Installation": [[35, "id1"]], "External Dependencies": [[35, "external-dependencies"]], "Methods and implementation": [[37, "methods-and-implementation"]], "BIDS Specification": [[37, null], [37, null], [37, null], [37, null], [37, null], [37, null]], "Fieldmap estimation: theory and methods": [[37, "fieldmap-estimation-theory-and-methods"]], "Direct B0 mapping sequences": [[37, "direct-b0-mapping-sequences"]], "Phase-difference B0 estimation": [[37, "phase-difference-b0-estimation"]], "PEPOLAR techniques": [[37, "pepolar-techniques"]], "Fieldmap-less approaches": [[37, "fieldmap-less-approaches"]], "Other (unsupported) approaches": [[37, "other-unsupported-approaches"]], "Estimation tooling": [[37, "estimation-tooling"]], "Unwarping the distorted data": [[37, "unwarping-the-distorted-data"]], "Discovering fieldmaps in a BIDS dataset": [[37, "discovering-fieldmaps-in-a-bids-dataset"]], "Explicit specification with B0FieldIdentifier": [[37, "explicit-specification-with-b0fieldidentifier"]], "Implicit specification with IntendedFor": [[37, "implicit-specification-with-intendedfor"]], "Fieldmap-less by registration to a T1-weighted image": [[37, "fieldmap-less-by-registration-to-a-t1-weighted-image"]], "References": [[37, "references"]]}, "indexentries": {"module": [[1, "module-sdcflows.cli"], [2, "module-sdcflows.cli.find_estimators"], [3, "module-sdcflows.data"], [4, "module-sdcflows.fieldmaps"], [5, "module-sdcflows.interfaces"], [6, "module-sdcflows.interfaces.brainmask"], [7, "module-sdcflows.interfaces.bspline"], [8, "module-sdcflows.interfaces.epi"], [9, "module-sdcflows.interfaces.fmap"], [10, "module-sdcflows.interfaces.reportlets"], [11, "module-sdcflows.interfaces.utils"], [12, "module-sdcflows.transform"], [13, "module-sdcflows.utils"], [14, "module-sdcflows.utils.bimap"], [15, "module-sdcflows.utils.epimanip"], [16, "module-sdcflows.utils.misc"], [17, "module-sdcflows.utils.phasemanip"], [18, "module-sdcflows.utils.tools"], [19, "module-sdcflows.utils.wrangler"], [20, "module-sdcflows.viz"], [21, "module-sdcflows.viz.utils"], [22, "module-sdcflows.workflows"], [23, "module-sdcflows.workflows.ancillary"], [24, "module-sdcflows.workflows.apply"], [25, "module-sdcflows.workflows.apply.correction"], [26, "module-sdcflows.workflows.apply.registration"], [27, "module-sdcflows.workflows.base"], [28, "module-sdcflows.workflows.fit"], [29, "module-sdcflows.workflows.fit.fieldmap"], [30, "module-sdcflows.workflows.fit.pepolar"], [31, "module-sdcflows.workflows.fit.syn"], [32, "module-sdcflows.workflows.outputs"]], "sdcflows.cli": [[1, "module-sdcflows.cli"]], "gen_layout() (in module sdcflows.cli.find_estimators)": [[2, "sdcflows.cli.find_estimators.gen_layout"]], "main() (in module sdcflows.cli.find_estimators)": [[2, "sdcflows.cli.find_estimators.main"]], "sdcflows.cli.find_estimators": [[2, "module-sdcflows.cli.find_estimators"]], "loader (class in sdcflows.data)": [[3, "sdcflows.data.Loader"]], "as_path() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.as_path"]], "as_path() (sdcflows.data.load method)": [[3, "sdcflows.data.load.as_path"]], "cached() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.cached"]], "cached() (sdcflows.data.load method)": [[3, "sdcflows.data.load.cached"]], "load() (in module sdcflows.data)": [[3, "sdcflows.data.load"]], "readable() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.readable"]], "readable() (sdcflows.data.load method)": [[3, "sdcflows.data.load.readable"]], "sdcflows.data": [[3, "module-sdcflows.data"]], "anat (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.ANAT"]], "estimatortype (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.EstimatorType"]], "fieldmapestimation (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.FieldmapEstimation"]], "fieldmapfile (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.FieldmapFile"]], "mapped (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.MAPPED"]], "metadataerror": [[4, "sdcflows.fieldmaps.MetadataError"]], "pepolar (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.PEPOLAR"]], "phasediff (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.PHASEDIFF"]], "unknown (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.UNKNOWN"]], "bids_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.bids_id"]], "bids_root (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.bids_root"]], "check_path() (sdcflows.fieldmaps.fieldmapfile method)": [[4, "sdcflows.fieldmaps.FieldmapFile.check_path"]], "clear_registry() (in module sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.clear_registry"]], "entities (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.entities"]], "find_meta (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.find_meta"]], "get_identifier() (in module sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.get_identifier"]], "get_workflow() (sdcflows.fieldmaps.fieldmapestimation method)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.get_workflow"]], "metadata (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.metadata"]], "method (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.method"]], "path (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.path"]], "paths() (sdcflows.fieldmaps.fieldmapestimation method)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.paths"]], "sdcflows.fieldmaps": [[4, "module-sdcflows.fieldmaps"]], "sources (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.sources"]], "suffix (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.suffix"]], "sdcflows.interfaces": [[5, "module-sdcflows.interfaces"]], "binarydilation (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.BinaryDilation"]], "brainextraction (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.BrainExtraction"]], "union (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.Union"]], "sdcflows.interfaces.brainmask": [[6, "module-sdcflows.interfaces.brainmask"]], "applycoeffsfield (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.ApplyCoeffsField"]], "bsplineapprox (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.BSplineApprox"]], "topupcoeffreorient (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.TOPUPCoeffReorient"]], "transformcoefficients (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.TransformCoefficients"]], "bspline_grid() (in module sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.bspline_grid"]], "sdcflows.interfaces.bspline": [[7, "module-sdcflows.interfaces.bspline"]], "getreadouttime (class in sdcflows.interfaces.epi)": [[8, "sdcflows.interfaces.epi.GetReadoutTime"]], "sortpeblips (class in sdcflows.interfaces.epi)": [[8, "sdcflows.interfaces.epi.SortPEBlips"]], "sdcflows.interfaces.epi": [[8, "module-sdcflows.interfaces.epi"]], "checkb0units (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.CheckB0Units"]], "checkregister (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.CheckRegister"]], "displacementsfield2fieldmap (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.DisplacementsField2Fieldmap"]], "phasemap2rads (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.PhaseMap2rads"]], "phasediff2fieldmap (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.Phasediff2Fieldmap"]], "subtractphases (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.SubtractPhases"]], "sdcflows.interfaces.fmap": [[9, "module-sdcflows.interfaces.fmap"]], "fieldmapreportlet (class in sdcflows.interfaces.reportlets)": [[10, "sdcflows.interfaces.reportlets.FieldmapReportlet"]], "sdcflows.interfaces.reportlets": [[10, "module-sdcflows.interfaces.reportlets"]], "convertwarp (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.ConvertWarp"]], "denoiseimage (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.DenoiseImage"]], "deoblique (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Deoblique"]], "flatten (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Flatten"]], "padslices (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.PadSlices"]], "positivedirectioncosines (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.PositiveDirectionCosines"]], "reoblique (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Reoblique"]], "reorientimageandmetadata (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.ReorientImageAndMetadata"]], "uniformgrid (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.UniformGrid"]], "sdcflows.interfaces.utils": [[11, "module-sdcflows.interfaces.utils"]], "b0fieldtransform (class in sdcflows.transform)": [[12, "sdcflows.transform.B0FieldTransform"]], "apply() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.apply"]], "coeffs (sdcflows.transform.b0fieldtransform attribute)": [[12, "sdcflows.transform.B0FieldTransform.coeffs"]], "disp_to_fmap() (in module sdcflows.transform)": [[12, "sdcflows.transform.disp_to_fmap"]], "fit() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.fit"]], "fmap_to_disp() (in module sdcflows.transform)": [[12, "sdcflows.transform.fmap_to_disp"]], "grid_bspline_weights() (in module sdcflows.transform)": [[12, "sdcflows.transform.grid_bspline_weights"]], "mapped (sdcflows.transform.b0fieldtransform attribute)": [[12, "sdcflows.transform.B0FieldTransform.mapped"]], "sdcflows.transform": [[12, "module-sdcflows.transform"]], "to_displacements() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.to_displacements"]], "unwarp_parallel() (in module sdcflows.transform)": [[12, "sdcflows.transform.unwarp_parallel"]], "worker() (in module sdcflows.transform)": [[12, "sdcflows.transform.worker"]], "sdcflows.utils": [[13, "module-sdcflows.utils"]], "estimatorregistry (class in sdcflows.utils.bimap)": [[14, "sdcflows.utils.bimap.EstimatorRegistry"]], "add() (sdcflows.utils.bimap.bidict method)": [[14, "sdcflows.utils.bimap.bidict.add"]], "bidict (class in sdcflows.utils.bimap)": [[14, "sdcflows.utils.bimap.bidict"]], "clear() (sdcflows.utils.bimap.bidict method)": [[14, "sdcflows.utils.bimap.bidict.clear"]], "get_key() (sdcflows.utils.bimap.estimatorregistry method)": [[14, "sdcflows.utils.bimap.EstimatorRegistry.get_key"]], "sdcflows.utils.bimap": [[14, "module-sdcflows.utils.bimap"]], "sources (sdcflows.utils.bimap.estimatorregistry property)": [[14, "sdcflows.utils.bimap.EstimatorRegistry.sources"]], "epi_mask() (in module sdcflows.utils.epimanip)": [[15, "sdcflows.utils.epimanip.epi_mask"]], "get_trt() (in module sdcflows.utils.epimanip)": [[15, "sdcflows.utils.epimanip.get_trt"]], "sdcflows.utils.epimanip": [[15, "module-sdcflows.utils.epimanip"]], "create_logger() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.create_logger"]], "front() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.front"]], "get_free_mem() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.get_free_mem"]], "last() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.last"]], "sdcflows.utils.misc": [[16, "module-sdcflows.utils.misc"]], "au2rads() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.au2rads"]], "delta_te() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.delta_te"]], "phdiff2fmap() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.phdiff2fmap"]], "sdcflows.utils.phasemanip": [[17, "module-sdcflows.utils.phasemanip"]], "subtract_phases() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.subtract_phases"]], "brain_masker() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.brain_masker"]], "deoblique_and_zooms() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.deoblique_and_zooms"]], "ensure_positive_cosines() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.ensure_positive_cosines"]], "reorient_pedir() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.reorient_pedir"]], "resample_to_zooms() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.resample_to_zooms"]], "sdcflows.utils.tools": [[18, "module-sdcflows.utils.tools"]], "find_anatomical_estimators() (in module sdcflows.utils.wrangler)": [[19, "sdcflows.utils.wrangler.find_anatomical_estimators"]], "find_estimators() (in module sdcflows.utils.wrangler)": [[19, "sdcflows.utils.wrangler.find_estimators"]], "sdcflows.utils.wrangler": [[19, "module-sdcflows.utils.wrangler"]], "sdcflows.viz": [[20, "module-sdcflows.viz"]], "coolwarm_transparent() (in module sdcflows.viz.utils)": [[21, "sdcflows.viz.utils.coolwarm_transparent"]], "plot_registration() (in module sdcflows.viz.utils)": [[21, "sdcflows.viz.utils.plot_registration"]], "sdcflows.viz.utils": [[21, "module-sdcflows.viz.utils"]], "sdcflows.workflows": [[22, "module-sdcflows.workflows"]], "init_brainextraction_wf() (in module sdcflows.workflows.ancillary)": [[23, "sdcflows.workflows.ancillary.init_brainextraction_wf"]], "sdcflows.workflows.ancillary": [[23, "module-sdcflows.workflows.ancillary"]], "sdcflows.workflows.apply": [[24, "module-sdcflows.workflows.apply"]], "init_unwarp_wf() (in module sdcflows.workflows.apply.correction)": [[25, "sdcflows.workflows.apply.correction.init_unwarp_wf"]], "sdcflows.workflows.apply.correction": [[25, "module-sdcflows.workflows.apply.correction"]], "init_coeff2epi_wf() (in module sdcflows.workflows.apply.registration)": [[26, "sdcflows.workflows.apply.registration.init_coeff2epi_wf"]], "sdcflows.workflows.apply.registration": [[26, "module-sdcflows.workflows.apply.registration"]], "init_fmap_preproc_wf() (in module sdcflows.workflows.base)": [[27, "sdcflows.workflows.base.init_fmap_preproc_wf"]], "sdcflows.workflows.base": [[27, "module-sdcflows.workflows.base"]], "sdcflows.workflows.fit": [[28, "module-sdcflows.workflows.fit"]], "init_fmap_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_fmap_wf"]], "init_magnitude_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_magnitude_wf"]], "init_phdiff_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_phdiff_wf"]], "sdcflows.workflows.fit.fieldmap": [[29, "module-sdcflows.workflows.fit.fieldmap"]], "init_3dqwarp_wf() (in module sdcflows.workflows.fit.pepolar)": [[30, "sdcflows.workflows.fit.pepolar.init_3dQwarp_wf"]], "init_topup_wf() (in module sdcflows.workflows.fit.pepolar)": [[30, "sdcflows.workflows.fit.pepolar.init_topup_wf"]], "sdcflows.workflows.fit.pepolar": [[30, "module-sdcflows.workflows.fit.pepolar"]], "init_syn_preprocessing_wf() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.init_syn_preprocessing_wf"]], "init_syn_sdc_wf() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.init_syn_sdc_wf"]], "match_histogram() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.match_histogram"]], "sdcflows.workflows.fit.syn": [[31, "module-sdcflows.workflows.fit.syn"]], "derivativesdatasink (class in sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.DerivativesDataSink"]], "init_fmap_derivatives_wf() (in module sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.init_fmap_derivatives_wf"]], "init_fmap_reports_wf() (in module sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.init_fmap_reports_wf"]], "out_path_base (sdcflows.workflows.outputs.derivativesdatasink attribute)": [[32, "sdcflows.workflows.outputs.DerivativesDataSink.out_path_base"]], "sdcflows.workflows.outputs": [[32, "module-sdcflows.workflows.outputs"]]}}) \ No newline at end of file +Search.setIndex({"docnames": ["api", "api/sdcflows.cli", "api/sdcflows.cli.find_estimators", "api/sdcflows.data", "api/sdcflows.fieldmaps", "api/sdcflows.interfaces", "api/sdcflows.interfaces.brainmask", "api/sdcflows.interfaces.bspline", "api/sdcflows.interfaces.epi", "api/sdcflows.interfaces.fmap", "api/sdcflows.interfaces.reportlets", "api/sdcflows.interfaces.utils", "api/sdcflows.transform", "api/sdcflows.utils", "api/sdcflows.utils.bimap", "api/sdcflows.utils.epimanip", "api/sdcflows.utils.misc", "api/sdcflows.utils.phasemanip", "api/sdcflows.utils.tools", "api/sdcflows.utils.wrangler", "api/sdcflows.viz", "api/sdcflows.viz.utils", "api/sdcflows.workflows", "api/sdcflows.workflows.ancillary", "api/sdcflows.workflows.apply", "api/sdcflows.workflows.apply.correction", "api/sdcflows.workflows.apply.registration", "api/sdcflows.workflows.base", "api/sdcflows.workflows.fit", "api/sdcflows.workflows.fit.fieldmap", "api/sdcflows.workflows.fit.pepolar", "api/sdcflows.workflows.fit.syn", "api/sdcflows.workflows.outputs", "changes", "index", "installation", "links", "methods"], "filenames": ["api.rst", "api/sdcflows.cli.rst", "api/sdcflows.cli.find_estimators.rst", "api/sdcflows.data.rst", "api/sdcflows.fieldmaps.rst", "api/sdcflows.interfaces.rst", "api/sdcflows.interfaces.brainmask.rst", "api/sdcflows.interfaces.bspline.rst", "api/sdcflows.interfaces.epi.rst", "api/sdcflows.interfaces.fmap.rst", "api/sdcflows.interfaces.reportlets.rst", "api/sdcflows.interfaces.utils.rst", "api/sdcflows.transform.rst", "api/sdcflows.utils.rst", "api/sdcflows.utils.bimap.rst", "api/sdcflows.utils.epimanip.rst", "api/sdcflows.utils.misc.rst", "api/sdcflows.utils.phasemanip.rst", "api/sdcflows.utils.tools.rst", "api/sdcflows.utils.wrangler.rst", "api/sdcflows.viz.rst", "api/sdcflows.viz.utils.rst", "api/sdcflows.workflows.rst", "api/sdcflows.workflows.ancillary.rst", "api/sdcflows.workflows.apply.rst", "api/sdcflows.workflows.apply.correction.rst", "api/sdcflows.workflows.apply.registration.rst", "api/sdcflows.workflows.base.rst", "api/sdcflows.workflows.fit.rst", "api/sdcflows.workflows.fit.fieldmap.rst", "api/sdcflows.workflows.fit.pepolar.rst", "api/sdcflows.workflows.fit.syn.rst", "api/sdcflows.workflows.outputs.rst", "changes.rst", "index.rst", "installation.rst", "links.rst", "methods.rst"], "titles": ["Library API (application program interface)", "sdcflows.cli package", "sdcflows.cli.find_estimators module", "sdcflows.data package", "sdcflows.fieldmaps module", "sdcflows.interfaces package", "sdcflows.interfaces.brainmask module", "sdcflows.interfaces.bspline module", "sdcflows.interfaces.epi module", "sdcflows.interfaces.fmap module", "sdcflows.interfaces.reportlets module", "sdcflows.interfaces.utils module", "sdcflows.transform module", "sdcflows.utils package", "sdcflows.utils.bimap module", "sdcflows.utils.epimanip module", "sdcflows.utils.misc module", "sdcflows.utils.phasemanip module", "sdcflows.utils.tools module", "sdcflows.utils.wrangler module", "sdcflows.viz package", "sdcflows.viz.utils module", "sdcflows.workflows package", "sdcflows.workflows.ancillary module", "sdcflows.workflows.apply package", "sdcflows.workflows.apply.correction module", "sdcflows.workflows.apply.registration module", "sdcflows.workflows.base module", "sdcflows.workflows.fit package", "sdcflows.workflows.fit.fieldmap module", "sdcflows.workflows.fit.pepolar module", "sdcflows.workflows.fit.syn module", "sdcflows.workflows.outputs module", "What\u2019s new?", "SDCFlows", "Installation", "<no title>", "Methods and implementation"], "terms": {"inform": [0, 33, 37], "specif": [0, 3, 4, 33, 34], "function": [0, 3, 12, 18, 19, 31, 33, 35, 37], "class": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 32], "method": [0, 3, 4, 12, 19, 29, 30, 31, 33, 34], "sdcflow": [0, 35, 37], "cli": [0, 33, 34], "packag": [0, 33, 34, 35], "submodul": [0, 33, 34, 37], "find_estim": [0, 1, 19, 37], "modul": [0, 1, 3, 5, 13, 20, 22, 24, 28, 33, 34], "gen_layout": [0, 2], "main": [0, 2], "data": [0, 4, 6, 7, 8, 11, 12, 15, 18, 19, 32, 33, 34], "load": [0, 3, 33, 34], "readabl": [0, 3], "as_path": [0, 3], "cach": [0, 3, 12, 33], "loader": [0, 3, 34], "fieldmap": [0, 7, 8, 9, 10, 12, 14, 17, 19, 23, 25, 26, 27, 28, 30, 31, 32, 33, 34], "estimatortyp": [0, 4, 19, 34], "anat": [0, 4, 19], "map": [0, 4, 7, 9, 11, 12, 14, 17, 19, 23, 25, 26, 29, 31, 32, 33, 34], "pepolar": [0, 4, 7, 19, 26, 28, 33, 34], "phasediff": [0, 4, 7, 9, 19, 29, 33, 37], "unknown": [0, 4], "fieldmapestim": [0, 4, 14, 19, 27, 33, 34], "bids_id": [0, 4, 19], "get_workflow": [0, 4], "path": [0, 3, 4, 7, 12, 16, 29, 30, 31, 32, 33, 35], "sourc": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 29, 30, 31, 32, 34, 37], "fieldmapfil": [0, 4, 19, 33, 34], "bids_root": [0, 4], "check_path": [0, 4], "entiti": [0, 4, 19, 32, 33], "find_meta": [0, 4], "metadata": [0, 4, 8, 9, 11, 12, 15, 17, 19, 25, 29, 30, 31, 32, 33, 37], "suffix": [0, 4, 19], "metadataerror": [0, 4, 34], "clear_registri": [0, 4, 19, 34], "get_identifi": [0, 4, 34], "brainmask": [0, 5, 23, 31], "binarydil": [0, 6], "brainextract": [0, 6], "union": [0, 6], "bspline": [0, 5, 33, 37], "applycoeffsfield": [0, 7, 33], "bsplineapprox": [0, 7, 33], "topupcoeffreori": [0, 7], "transformcoeffici": [0, 7], "bspline_grid": [0, 7], "epi": [0, 5, 6, 7, 11, 12, 15, 18, 19, 23, 25, 26, 30, 31, 33, 34, 37], "getreadouttim": [0, 8], "sortpeblip": [0, 8], "fmap": [0, 3, 4, 5, 26, 27, 29, 30, 31], "checkb0unit": [0, 9], "checkregist": [0, 9], "displacementsfield2fieldmap": [0, 9], "phasemap2rad": [0, 9], "phasediff2fieldmap": [0, 9], "subtractphas": [0, 9], "reportlet": [0, 5, 33], "fieldmapreportlet": [0, 10, 33], "util": [0, 4, 5, 12, 20, 33, 34, 37], "convertwarp": [0, 11], "denoiseimag": [0, 11], "deobliqu": [0, 11, 37], "flatten": [0, 11, 14, 30], "padslic": [0, 11], "positivedirectioncosin": [0, 11], "reobliqu": [0, 11], "reorientimageandmetadata": [0, 11], "uniformgrid": [0, 11], "transform": [0, 7, 9, 18, 26, 31, 34, 37], "b0fieldtransform": [0, 7, 12, 34], "appli": [0, 7, 12, 19, 22, 29, 30, 31, 33, 37], "coeff": [0, 12], "fit": [0, 7, 12, 22, 33, 37], "to_displac": [0, 12], "disp_to_fmap": [0, 12, 34], "fmap_to_disp": [0, 12, 34], "grid_bspline_weight": [0, 7, 12, 34], "unwarp_parallel": [0, 12, 34], "worker": [0, 12, 34], "bimap": [0, 13], "estimatorregistri": [0, 14], "get_kei": [0, 14], "bidict": [0, 14], "add": [0, 11, 14, 33], "clear": [0, 14, 37], "epimanip": [0, 13], "epi_mask": [0, 15, 31], "get_trt": [0, 15], "misc": [0, 13], "create_logg": [0, 16], "front": [0, 16, 33, 37], "get_free_mem": [0, 16], "last": [0, 4, 14, 15, 16, 17, 33], "phasemanip": [0, 13], "au2rad": [0, 17], "delta_t": [0, 17], "phdiff2fmap": [0, 17], "subtract_phas": [0, 17], "tool": [0, 12, 13, 21, 33, 34, 35], "brain_mask": [0, 18], "deoblique_and_zoom": [0, 18], "ensure_positive_cosin": [0, 18], "reorient_pedir": [0, 18], "resample_to_zoom": [0, 18], "wrangler": [0, 13, 33, 37], "find_anatomical_estim": [0, 19], "viz": [0, 34], "coolwarm_transpar": [0, 21], "plot_registr": [0, 21], "workflow": [0, 4, 19, 33, 34, 37], "subpackag": [0, 34], "correct": [0, 7, 11, 12, 24, 29, 33, 34, 37], "init_unwarp_wf": [0, 25], "registr": [0, 9, 10, 12, 24, 31, 33, 34], "init_coeff2epi_wf": [0, 26], "init_fmap_wf": [0, 29], "init_magnitude_wf": [0, 29], "init_phdiff_wf": [0, 29], "init_3dqwarp_wf": [0, 30], "init_topup_wf": [0, 30, 33], "syn": [0, 7, 11, 28, 33, 37], "init_syn_preprocessing_wf": [0, 31, 37], "init_syn_sdc_wf": [0, 31, 37], "match_histogram": [0, 31], "ancillari": [0, 22], "init_brainextraction_wf": [0, 23], "base": [0, 4, 6, 7, 8, 9, 10, 11, 12, 14, 22, 29, 30, 31, 32, 34, 35, 37], "init_fmap_preproc_wf": [0, 27, 33], "output": [0, 6, 7, 8, 9, 10, 11, 12, 22, 23, 25, 26, 27, 29, 30, 31, 33, 37], "derivativesdatasink": [0, 32, 33], "out_path_bas": [0, 32], "init_fmap_derivatives_wf": [0, 32], "init_fmap_reports_wf": [0, 32], "bids_dir": 2, "database_dir": 2, "none": [2, 4, 6, 7, 8, 9, 11, 12, 14, 15, 17, 18, 19, 21, 25, 31, 32, 37], "argv": 2, "pars": 2, "bid": [2, 4, 8, 9, 15, 17, 19, 29, 32, 33, 34], "directori": [2, 3, 27, 32], "print": [2, 35], "subject": [2, 19, 27, 33], "estim": [2, 4, 7, 11, 12, 14, 19, 23, 26, 27, 29, 30, 31, 32, 33, 34], "file": [3, 4, 6, 7, 8, 9, 10, 11, 12, 19, 23, 26, 30, 31, 32, 33, 35], "segment": [3, 37], "rel": [3, 33, 35], "thi": [3, 4, 7, 9, 11, 12, 15, 18, 19, 25, 26, 27, 29, 30, 31, 33, 34, 37], "contain": [3, 12, 14, 19, 29, 30, 32, 33, 37], "follow": [3, 7, 12, 15, 18, 33, 35, 37], "top": 3, "level": [3, 12, 16, 19, 33, 37], "affin": [3, 7, 9, 12, 33], "json": [3, 4, 15], "flirtsch": 3, "any_registr": 3, "any_registration_test": 3, "fmap_atla": 3, "nii": [3, 4, 9, 15, 29], "gz": [3, 4, 9, 15, 29], "fmap_atlas_2_mni152nlin2009casym_affin": 3, "mat": 3, "sd_syn": 3, "sd_syn_sloppi": 3, "translation_rigid": 3, "travers": 3, "provid": [3, 4, 12, 15, 19, 29, 33, 34, 37], "read": [3, 4, 17], "access": [3, 33, 34], "resourc": [3, 33], "through": [3, 7, 9, 11, 12, 33], "like": [3, 12, 31], "interfac": [3, 4, 18, 33, 34, 37], "mai": [3, 4, 7, 9, 12, 15, 25, 26, 27, 29, 34, 37], "exist": [3, 6, 7, 8, 9, 10, 11, 32, 37], "filesystem": 3, "effici": [3, 33], "us": [3, 4, 7, 9, 11, 12, 15, 18, 19, 25, 26, 27, 29, 31, 33, 35, 37], "oper": [3, 12, 15, 18, 33], "includ": [3, 12, 19, 33, 37], "result": [3, 7, 12, 33, 37], "i": [3, 4, 7, 8, 9, 11, 12, 14, 15, 18, 19, 21, 26, 29, 31, 33, 34, 35, 37], "copi": [3, 11, 33], "case": [3, 7, 9, 19, 26, 33, 37], "where": [3, 7, 9, 10, 12, 15, 31, 37], "would": 3, "necessari": [3, 11, 15, 19, 29, 33, 37], "abstractcontextmanag": 3, "ensur": [3, 9, 11, 29, 33], "avail": [3, 4, 8, 15, 19, 33, 35, 37], "gener": [3, 7, 9, 10, 12, 14, 18, 26, 27, 29, 33], "context": [3, 33], "manag": 3, "yield": [3, 37], "when": [3, 4, 7, 12, 19, 29, 33, 37], "enter": 3, "ani": [3, 8, 9, 11, 12, 19, 32, 37], "temporari": [3, 12], "ar": [3, 4, 7, 8, 9, 11, 12, 15, 18, 19, 29, 30, 31, 32, 33, 34, 35, 37], "creat": [3, 7, 12, 19, 27, 30, 31, 33], "delet": 3, "exit": 3, "remain": 3, "throughout": 3, "durat": 3, "program": [3, 11, 33, 34], "python": [3, 33, 34, 35], "so": [3, 7, 8, 9, 31, 33, 37], "multipl": [3, 30, 33, 37], "call": [3, 4, 7, 12, 14, 15, 17, 25, 33], "do": [3, 12, 15, 33, 37], "unpack": 3, "same": [3, 7, 9, 11, 12, 33, 37], "time": [3, 7, 8, 9, 11, 12, 15, 25, 33, 37], "sensit": [3, 33], "argument": [3, 4, 11, 19, 33, 37], "": [3, 4, 7, 8, 9, 11, 12, 14, 15, 19, 25, 29, 30, 31, 32, 34, 35, 37], "pass": [3, 9, 18, 19, 33, 37], "anchor": 3, "str": [3, 4, 11, 12, 16, 19, 23, 25, 26, 27, 29, 30, 31, 32], "A": [3, 4, 7, 10, 11, 12, 14, 18, 19, 27, 29, 30, 31, 32, 33, 35, 37], "wrap": [3, 9, 11, 12, 29, 37], "importlib": 3, "getter": 3, "an": [3, 6, 7, 8, 9, 10, 11, 12, 14, 15, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37], "interpret": [3, 35, 37], "lifetim": 3, "scope": 3, "For": [3, 12, 15, 18, 19, 29, 37], "typic": [3, 12, 34, 37], "simpli": 3, "object": [3, 4, 6, 7, 8, 9, 10, 11, 12, 19, 32, 33], "zip": 3, "distribut": [3, 7], "clean": [3, 19], "up": [3, 25, 31, 32, 33, 35, 37], "accept": [3, 18, 33], "fulli": [3, 7, 18], "qualifi": 3, "name": [3, 4, 10, 15, 16, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33], "expect": [3, 9, 11, 31], "usag": 3, "autofunct": 3, "load_data": 3, "automethod": 3, "from": [3, 4, 7, 8, 9, 11, 12, 15, 16, 17, 18, 19, 23, 25, 29, 31, 32, 33, 35, 37], "import": [3, 18, 19, 33, 35], "__package__": 3, "implement": [3, 7, 12, 15, 33, 34], "callabl": [3, 12], "docstr": [3, 33], "intend": [3, 11], "treat": [3, 11], "document": [3, 15, 33], "greater": 3, "flexibl": [3, 37], "improv": [3, 33], "over": [3, 12, 15, 33], "explicit": [3, 34], "On": [3, 35], "true": [3, 4, 7, 9, 11, 12, 14, 18, 19, 31, 32, 37], "fals": [3, 4, 7, 9, 10, 11, 12, 19, 21, 25, 26, 27, 29, 30, 31, 32], "n": [3, 11, 12, 37], "It": [3, 15, 37], "also": [3, 7, 19, 25, 31, 33, 37], "possibl": [3, 15, 19, 37], "directli": [3, 7, 12, 29, 33, 37], "other_packag": 3, "ext": 3, "read_text": 3, "pkgdata": 3, "requir": [3, 29, 33, 34, 35], "full": [3, 12, 21], "func": [3, 12], "contrast": [3, 31], "importlib_resourc": 3, "as_fil": 3, "joinpath": 3, "valu": [4, 6, 7, 8, 9, 10, 11, 12, 14, 19, 32, 33], "enum": 4, "repres": [4, 6, 7, 8, 9, 10, 11, 12, 32, 37], "differ": [4, 9, 15, 17, 19, 29, 33, 34], "type": [4, 8, 9, 12, 14, 19, 32, 37], "approach": [4, 19, 33, 34], "5": [4, 7, 12, 18, 19, 34, 35, 37], "4": [4, 7, 11, 12, 14, 15, 18, 19, 34, 37], "2": [4, 7, 9, 11, 12, 14, 15, 19, 34, 35, 37], "3": [4, 6, 7, 11, 12, 14, 15, 18, 19, 31, 34, 35, 37], "1": [4, 7, 9, 10, 11, 12, 14, 15, 16, 18, 19, 25, 29, 30, 31, 34, 35, 37], "strategi": [4, 7, 12, 27, 33, 37], "consist": [4, 8, 9, 11, 33, 37], "all": [4, 7, 9, 11, 12, 14, 18, 19, 33, 35], "The": [4, 6, 7, 9, 11, 12, 15, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37], "actual": [4, 7, 25, 29], "infer": [4, 11], "input": [4, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 37], "collect": [4, 33], "uniqu": [4, 25, 26, 29], "b0fieldidentifi": [4, 19, 27, 32, 33, 34], "field": [4, 7, 9, 11, 12, 15, 19, 25, 26, 27, 29, 30, 31, 32, 33, 37], "kwarg": [4, 10, 14], "build": [4, 31, 32, 33, 35, 37], "correspond": [4, 7, 8, 9, 11, 19, 25, 26, 29, 30, 31, 33, 34, 37], "instanc": [4, 18, 19, 33, 37], "flag": 4, "indic": [4, 11, 19], "return": [4, 12, 14, 16, 18, 19, 33], "tupl": [4, 7, 11, 12, 16, 29, 31], "sort": [4, 8, 23, 33], "list": [4, 7, 8, 9, 11, 12, 14, 16, 19, 25, 27, 29, 30, 31, 32], "noth": 4, "bool": [4, 12, 19, 25, 26, 27, 29, 30, 31, 32], "can": [4, 7, 11, 12, 15, 18, 19, 26, 29, 35, 37], "some": [4, 15, 19, 23, 29, 33, 35, 37], "sidecar": [4, 15], "filenam": [4, 10, 11, 32], "match": [4, 7, 31], "receiv": [4, 37], "keyword": 4, "initi": [4, 19, 33], "exampl": [4, 14, 16, 17, 19], "f": [4, 7, 12, 15, 17, 33], "dsa_dir": 4, "sub": 4, "01": [4, 7, 19, 34], "01_t1w": 4, "t1w": [4, 19, 31, 33, 37], "01_dir": 4, "lr_epi": 4, "traceback": [4, 14, 15, 17], "most": [4, 12, 14, 15, 17, 18, 33, 37], "recent": [4, 7, 14, 15, 17, 29], "totalreadouttim": [4, 15], "0": [4, 7, 9, 10, 11, 12, 15, 16, 17, 18, 21, 25, 29, 30, 31, 34, 35, 37], "005": 4, "006": 4, "01_phasediff": 4, "echotime2": [4, 17, 29], "00746": 4, "01_phase2": 4, "echotim": [4, 29], "01_fieldmap": 4, "unit": [4, 9, 12, 17, 25, 29, 32, 33], "rad": [4, 9, 17, 33], "root": [4, 7, 33], "attribut": 4, "valid": [4, 12, 15, 19, 33], "extract": [4, 6, 11, 23, 32, 33], "filepath": 4, "enabl": [4, 7, 27, 33], "disabl": 4, "autom": [4, 37], "search": [4, 19, 37], "associ": [4, 12, 19, 31, 37], "overwrit": 4, "except": [4, 19], "valueerror": [4, 14, 15, 17], "better": [4, 15, 33], "error": [4, 7, 15, 33, 37], "empti": [4, 11, 14, 19], "registri": [4, 19, 33], "intendedfor": [4, 19, 33, 34], "identifi": [4, 12, 19, 33, 37], "given": [4, 9, 12, 17, 19, 23, 25, 30, 31, 33, 37], "paramet": [4, 9, 11, 12, 15, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 37], "we": [4, 7, 9, 12, 19, 29, 33, 37], "want": [4, 12, 37], "index": [4, 11, 12, 30], "tabl": 4, "which": [4, 7, 8, 9, 11, 12, 15, 27, 30, 32, 33, 37], "should": [4, 9, 10, 11, 12, 15, 18, 19, 29, 30, 31, 32, 33, 37], "perform": [4, 18, 26, 33, 37], "brain": [6, 7, 9, 10, 15, 23, 26, 29, 31, 32, 33, 37], "from_fil": [6, 7, 8, 9, 11], "resource_monitor": [6, 7, 8, 9, 11], "simpleinterfac": [6, 7, 8, 9, 11], "gre": [6, 23, 29, 37], "mandatori": [6, 7, 8, 9, 10, 11, 19, 32], "in_fil": [6, 8, 9, 11, 15, 17, 18, 23, 32], "pathlik": [6, 7, 8, 9, 10, 11, 12, 29, 32], "string": [6, 7, 8, 9, 10, 11, 19, 32], "binari": [6, 11, 29, 35], "dilat": 6, "option": [6, 7, 8, 9, 10, 11, 12, 15, 19, 23, 27, 30, 31, 32, 33, 37], "radiu": [6, 9], "float": [6, 7, 8, 9, 10, 12, 18, 31], "structur": [6, 12, 19, 33, 37], "element": [6, 16, 30, 31], "ball": 6, "nipyp": [6, 7, 9, 10, 11, 32, 33, 34, 35], "default": [6, 7, 9, 10, 11, 12, 21, 23, 27, 29, 32, 33, 37], "out_fil": [6, 9, 11, 15, 18, 23, 32], "after": [6, 7, 11, 12, 19, 23, 25, 29, 30, 33], "mask": [6, 7, 10, 11, 15, 18, 23, 25, 26, 29, 30, 31, 32, 33], "out_mask": [6, 11, 23], "out_probseg": [6, 23], "probabilist": 6, "in1": 6, "in2": 6, "filter": [7, 12, 19, 33, 37], "b_0": [7, 12, 15, 29, 33, 37], "b": [7, 12, 14, 18, 19, 23, 25, 29, 30, 31, 33, 37], "spline": [7, 12, 23, 25, 29, 30, 31, 33, 37], "undistort": 7, "target": [7, 12, 18, 25, 26, 32, 33, 37], "distort": [7, 12, 19, 25, 26, 31, 33, 34], "imag": [7, 8, 9, 11, 12, 15, 18, 19, 23, 25, 26, 29, 31, 33, 34], "formal": [7, 12], "its": [7, 25, 29, 32, 37], "coeffici": [7, 12, 25, 26, 27, 29, 30, 31, 32, 33, 37], "precondit": 7, "have": [7, 9, 11, 12, 18, 19, 21, 29, 30, 31, 33, 37], "bold": [7, 19, 31, 33, 37], "dwi": [7, 19, 33, 37], "dataset": [7, 11, 12, 19, 25, 26, 30, 32, 33, 34], "even": [7, 11], "mprage": 7, "principl": 7, "without": [7, 9, 11, 31, 33], "gone": 7, "hmc": [7, 12], "sdc": [7, 12, 19, 23, 27, 33, 37], "matric": [7, 12, 25, 33], "account": [7, 15, 18, 37], "head": [7, 12, 25], "motion": [7, 12, 25], "resampl": [7, 11, 12, 18, 26, 31, 33], "doe": [7, 12, 15], "move": [7, 10, 12, 26, 33], "anymor": 7, "align": [7, 12, 18, 26, 33, 37], "e": [7, 9, 12, 14, 15, 18, 31, 32, 33], "g": [7, 9, 15, 31, 32, 33], "magnitud": [7, 9, 23, 26, 29, 32, 33, 37], "et": [7, 37], "al": [7, 18, 37], "refer": [7, 10, 11, 12, 18, 19, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34], "algorithm": [7, 33, 37], "first": [7, 11, 15, 30, 31, 33, 37], "grid": [7, 12, 18, 25, 30, 33], "project": [7, 18, 37], "onto": [7, 12, 37], "space": [7, 12, 15, 25, 26, 31, 32, 33, 37], "reconstruct": [7, 12, 15, 37], "abov": [7, 29, 35], "second": [7, 12, 15, 31, 37], "step": [7, 12, 37], "find": [7, 15, 19, 33, 37], "locat": [7, 12, 32, 37], "everi": [7, 12, 37], "voxel": [7, 12, 18, 23, 25, 31, 37], "each": [7, 12, 30], "timepoint": [7, 31], "mean": [7, 9, 19, 37], "progress": 7, "reced": 7, "along": [7, 15, 25, 33, 37], "phase": [7, 9, 12, 17, 19, 29, 30, 31, 33, 34], "encod": [7, 9, 12, 19, 30, 31, 33, 37], "axi": [7, 11, 12, 37], "coordin": [7, 11, 12, 18, 37], "With": [7, 15, 33], "those": [7, 37], "known": [7, 15], "interpol": [7, 12, 25, 33, 37], "trivial": 7, "spatial": [7, 11, 12], "new": [7, 14, 18, 34], "in_coeff": 7, "item": [7, 8, 9, 11, 14, 32], "calcul": [7, 8, 9, 12, 15, 17, 23, 25, 27, 29, 31, 33, 37], "stage": [7, 37], "in_data": [7, 8, 11, 30], "pe_dir": [7, 8, 9, 11, 12, 18], "j": [7, 8, 9, 11, 12, 15, 18, 33, 37], "k": [7, 8, 9, 11, 12, 18, 37], "direct": [7, 8, 9, 11, 15, 18, 19, 30, 31, 33, 34], "ro_tim": [7, 9, 12], "readout": [7, 8, 9, 12, 15, 25, 37], "approx": [7, 12, 15], "boolean": [7, 9, 10, 11, 32], "origin": [7, 11, 12, 32, 33], "rotat": [7, 9, 18, 33, 37], "rather": [7, 12, 33, 37], "than": [7, 33], "data2fmap_xfm": 7, "mutual": [7, 11, 37], "exclus": [7, 11, 19], "m": [7, 35, 37], "p": [7, 37], "d": [7, 11, 14, 33], "t": [7, 12, 15, 17, 37], "_": [7, 14], "x": [7, 8, 11, 21, 34], "fmap2data_xfm": 7, "in_xfm": 7, "num_thread": [7, 11, 12], "integ": [7, 11, 23, 37], "number": [7, 11, 12, 15, 18, 25, 26, 27, 29, 30, 31, 33, 37], "thread": [7, 11, 25, 26, 27, 29, 33], "out_correct": 7, "out_field": [7, 11], "approxim": [7, 12, 31, 33], "tensor": [7, 12, 33, 37], "product": [7, 12, 18, 33], "effect": [7, 15, 33, 37], "smooth": [7, 37], "remov": [7, 12, 23, 29, 33], "spike": 7, "other": [7, 12, 18, 19, 33, 34, 35], "nois": [7, 11, 29], "well": [7, 33, 37], "extrapol": [7, 12, 33], "beyond": 7, "allevi": 7, "boundari": 7, "resolv": [7, 33], "optim": [7, 33, 37], "problem": [7, 15, 33, 37], "obtain": [7, 15, 18, 37], "c": [7, 12, 14, 35], "mathbf": [7, 12], "best": 7, "sampl": [7, 12, 18], "within": [7, 15, 33, 37], "eq": [7, 12, 15, 37], "17": [7, 37], "2d": 7, "unser1999": [7, 12], "here": [7, 12, 15, 18, 37], "3d": [7, 11, 37], "formul": [7, 15], "adapt": [7, 33], "unser": 7, "perfect": 7, "signal": 7, "process": [7, 18, 25, 26, 27, 29, 34, 37], "ieee": [7, 37], "magazin": 7, "16": [7, 34, 35, 37], "6": [7, 9, 12, 29, 34, 35, 37], "22": [7, 34], "38": 7, "1999": 7, "evalu": [7, 12, 33, 37], "cubic": [7, 12], "psi": [7, 12], "bs_space": 7, "form": [7, 11, 12, 18, 33], "between": [7, 37], "control": [7, 12, 26], "point": [7, 12, 37], "40": [7, 16], "20": [7, 34, 37], "debug": [7, 25, 26, 27, 29, 30, 31, 33], "extra": [7, 32], "asset": 7, "outsid": [7, 10, 12], "in_mask": [7, 11], "mode": [7, 12, 25, 26, 29, 30, 31, 33, 37], "median": 7, "ridge_alpha": 7, "regular": [7, 12, 31], "zooms_min": 7, "legal": 7, "limit": [7, 33], "minimum": [7, 33], "zoom": [7, 18, 33, 37], "set": [7, 12, 15, 19, 25, 31, 32, 33, 35, 37], "out_coeff": 7, "out_error": 7, "out_extrapol": 7, "revis": [7, 33], "orient": [7, 18, 33], "topup": [7, 8, 11, 30, 33, 37], "fieldcoeff": [7, 33], "just": [7, 12, 23, 29], "shape": [7, 9, 12, 33], "fixat": 7, "decim": 7, "factor": [7, 11, 15, 18, 29, 37], "ad": [7, 33], "pixel": [7, 15], "dimens": [7, 11, 12], "one": [7, 9, 12, 18, 19, 29, 33, 37], "reason": [7, 33], "why": 7, "fsl": [7, 8, 15, 29, 30, 33, 35, 37], "segfault": [7, 11], "ha": [7, 12, 15, 18, 19, 33, 37], "odd": [7, 33], "more": [7, 9, 19, 29, 31, 32, 33, 37], "These": [7, 19, 35, 37], "zero": [7, 10, 19, 33], "center": [7, 15, 33], "plumb": [7, 11, 33], "cardin": [7, 33], "ax": [7, 11, 12, 18, 33, 37], "q": 7, "nifti": [7, 11, 12, 19, 32, 37], "alwai": 7, "diagon": 7, "henc": 7, "director": 7, "cosin": [7, 11, 18], "posit": [7, 11, 18, 37], "In": [7, 9, 12, 18, 37], "word": [7, 12, 18], "either": [7, 29], "ra": [7, 12, 18, 33], "asr": 7, "sar": 7, "sra": 7, "modifi": [7, 21, 33], "fledg": 7, "therefor": [7, 12, 18, 30, 37], "header": [7, 11, 32, 33], "updat": [7, 9, 12, 18, 33, 37], "becaus": [7, 15, 19, 37], "obliqu": [7, 11, 18, 33, 37], "retain": 7, "mark": 7, "code": [7, 11, 25, 26, 29, 30, 31, 33], "fmap_ref": [7, 26, 27, 29, 30, 31, 32], "y": [7, 8, 11, 21, 33], "z": [7, 8, 11, 21, 33], "patch": [7, 33], "anoth": [7, 14], "rigid": 7, "bodi": 7, "fmap_target": 7, "feed": 7, "img": [7, 15, 18], "control_zooms_mm": 7, "nifti1imag": [7, 12], "embed": [7, 12], "deal": [8, 9], "variou": [8, 9], "dictionari": [8, 9, 11, 14, 19, 25, 30, 31, 32], "kei": [8, 9, 11, 14, 19, 32, 33], "pe_dir_fsl": 8, "pe_direct": 8, "readout_tim": 8, "pe": [8, 15, 25, 30, 31, 37], "blip": [8, 33], "thei": [8, 33, 37], "fed": [8, 30, 37], "pe_dirs_fsl": 8, "convent": 8, "total": [8, 9, 12, 15, 37], "out_data": [8, 11], "hz": [9, 10, 12, 17, 25, 29, 32, 33, 37], "check": [9, 11, 33, 35], "pair": [9, 14, 19, 29, 33], "phase1": [9, 29, 33], "phase2": [9, 29], "fmap_fil": 9, "_phase1": 9, "_phase2": 9, "mag_fil": 9, "_magnitude1": 9, "_magnitude2": 9, "_phasediff": 9, "_fieldmap": [9, 29], "_magnitud": 9, "If": [9, 11, 12, 15, 19, 31, 37], "two": [9, 15, 17, 18, 19, 29, 30, 33, 37], "regist": [9, 12, 33], "them": 9, "inspect": 9, "evid": 9, "significantli": 9, "fov": [9, 33], "02rad": 9, "1mm": 9, "both": [9, 10, 18, 33, 37], "shift": [9, 12, 15, 37], "assum": [9, 31, 37], "50mm": 9, "run": [9, 11, 19, 25, 26, 29, 30, 31, 33], "mri_robust_regist": 9, "submit": [9, 33], "diff": 9, "verifi": 9, "rot_thresh": 9, "threshold": [9, 31], "radian": [9, 37], "02": 9, "trans_thresh": 9, "translat": 9, "mm": [9, 31], "convert": [9, 11, 12, 17, 29, 33, 37], "b0": [9, 34], "displac": [9, 11, 12, 25, 31, 33, 37], "demean": [9, 33], "regress": 9, "itk_transform": 9, "whether": [9, 18, 25, 29, 30, 31, 32], "itk": [9, 11, 12, 25, 26], "ant": [9, 11, 12, 26, 33, 35, 37], "u": [9, 17], "4096": 9, "rang": [9, 12, 29, 33, 37], "28": [9, 29, 33], "in_meta": [9, 11, 15, 17, 31], "in_phas": [9, 17], "phase_diff": 9, "special": [10, 14], "reportcapableinterfac": 10, "abstract": 10, "mixin": 10, "apply_mask": 10, "max_alpha": [10, 21], "maximum": [10, 12, 25, 26, 27, 29, 33], "alpha": 10, "channel": [10, 37], "7": [10, 21, 34, 37], "moving_label": 10, "label": [10, 12, 15, 19, 21, 27, 33, 37], "mosaic": 10, "out_report": 10, "visual": [10, 21, 33, 37], "report": [10, 15, 32, 33], "svg": [10, 25, 26, 29, 30, 31], "reference_label": 10, "show": [10, 33], "shown": 10, "3dqwarp": [11, 30, 33, 37], "compat": [11, 12, 33, 37], "warp": [11, 31, 37], "copyheaderinterfac": 11, "execut": [11, 12, 19, 31, 37], "copy_head": 11, "capabl": 11, "input_imag": 11, "scalar": 11, "command": [11, 35], "line": [11, 35], "save_nois": 11, "save": [11, 27, 32, 33], "noise_imag": 11, "arg": [11, 14], "addit": [11, 18, 26, 35], "forc": [11, 19, 37], "specifi": [11, 31, 33], "dimension": [11, 37], "tri": 11, "environ": [11, 35], "byte": [11, 19], "variabl": 11, "noise_model": 11, "gaussian": 11, "rician": 11, "emploi": 11, "model": [11, 37], "output_imag": 11, "version": [11, 33, 35], "o": [11, 12, 29, 32, 37], "shrink_factor": 11, "larg": [11, 33], "consum": 11, "To": [11, 19, 33, 37], "lessen": 11, "comput": [11, 12, 31], "shrink": 11, "singl": [11, 12, 19, 27, 33, 37], "describ": [11, 33, 37], "verbos": [11, 33], "v": [11, 37], "make": [11, 33, 35, 37], "potenti": [11, 33], "4d": [11, 12, 33], "max_tr": 11, "onli": [11, 12, 18, 19, 33, 37], "pick": [11, 19], "tr": 11, "50": [11, 33], "out_list": 11, "out_meta": [11, 32], "uneven": 11, "slice": [11, 33, 37], "avoid": [11, 33], "chang": [11, 19, 33], "standard": [11, 15, 33], "configur": [11, 12, 26, 30, 31], "stack": 11, "pad": [11, 18, 33], "wa": [11, 12, 29, 30, 31, 32], "reorient": [11, 18, 33], "polar": [11, 18, 33, 37], "in_orient": 11, "in_epi": [11, 31], "in_field": 11, "in_plumb": 11, "out_epi": 11, "target_orient": 11, "system": [11, 18, 35], "unwarp": [12, 25, 30, 31, 33, 34], "deform": [12, 31, 37], "caus": 12, "suscept": [12, 19, 31, 33, 34, 37], "deriv": [12, 27, 32, 33, 34, 37], "attempt": [12, 19, 37], "represent": [12, 33, 37], "independ": 12, "see": [12, 19, 33, 37], "That": 12, "achiev": 12, "multi": [12, 19, 37], "linear": [12, 37], "combin": [12, 27], "basi": [12, 37], "eqref": [12, 15, 37], "sum_": 12, "k_1": 12, "k_2": 12, "k_3": 12, "tag": [12, 15, 33, 37], "spatialimag": [12, 18, 33], "sequenc": [12, 29, 34], "xfm": [12, 18], "ndarrai": 12, "xfm_data2fmap": 12, "order": [12, 18, 21, 33], "int": [12, 16, 18, 23, 25, 26, 27, 29, 30, 31], "constant": 12, "cval": 12, "prefilt": [12, 18], "output_dtyp": 12, "dtype": [12, 32], "allow_neg": 12, "handl": [12, 33, 35], "parallel": [12, 15, 30, 31, 37], "phaseencodingdirect": [12, 15, 18, 19], "scan": [12, 15, 34, 37], "express": [12, 37], "physic": [12, 37], "realign": 12, "seri": [12, 34], "volum": [12, 30, 31, 33], "numpi": [12, 32], "target_refer": 12, "12": [12, 34], "degre": 12, "freedom": 12, "carri": 12, "target_affin": 12, "framework": [12, 33, 37], "our": [12, 19, 33], "reflect": 12, "nearest": 12, "mirror": 12, "determin": [12, 18], "how": [12, 15, 19, 35, 37], "extend": 12, "overflow": 12, "border": 12, "arrai": [12, 18, 37], "befor": [12, 33], "float64": 12, "slightli": 12, "blur": 12, "unless": [12, 33], "overrid": [12, 33], "instead": [12, 33], "propag": [12, 32], "upper": 12, "bound": 12, "memori": [12, 16, 33], "neg": 12, "introduc": [12, 37], "happen": 12, "nonneg": 12, "gt": 12, "your": [12, 35], "per": [12, 15, 19, 29, 33], "matrix": [12, 15, 33], "vsm": [12, 33, 37], "extent": [12, 18], "fourth": 12, "drop": [12, 33], "intern": [12, 30, 31], "reus": [12, 33], "itk_format": 12, "section": [12, 37], "nibabel": [12, 18], "xyz_nii": 12, "invers": [12, 18, 31], "previou": [12, 33, 37], "format": [12, 25, 37], "fmap_nii": 12, "target_nii": 12, "ctrl_nii": 12, "float32": 12, "weight": [12, 34], "s_1": 12, "s_2": 12, "s_3": 12, "knot": 12, "kernel": [12, 33], "beta": 12, "cdot": [12, 15, 37], "1d": 12, "piecewis": 12, "close": 12, "By": [12, 37], "iter": 12, "fall": 12, "compact": [12, 37], "support": [12, 29, 30, 31, 33], "out": [12, 32, 33], "dismiss": [12, 19], "lighten": 12, "final": [12, 19, 33, 34], "easili": [12, 34], "design": [12, 33, 34], "spars": 12, "async": 12, "fulldataset": 12, "fmap_hz": 12, "pe_info": 12, "max_concurr": 12, "across": [12, 30, 31, 33], "sign": 12, "must": [12, 19, 30, 35], "revers": [12, 14, 15, 37], "obj": [12, 29], "hmc_xfm": 12, "semaphor": 12, "attach": 12, "loop": 12, "bidirect": 14, "hashmap": 14, "track": 14, "file3": 14, "txt": 14, "file4": 14, "file1": 14, "file2": 14, "auto_00000": [14, 19], "auto_00002": [14, 19], "file5": 14, "get": [14, 15, 33], "particular": [14, 29], "properti": [14, 18], "dict": [14, 17, 19, 29, 30, 31, 32], "del": 14, "typeerror": 14, "self": [14, 33], "keyerror": 14, "alreadi": [14, 29, 33, 37], "unhash": 14, "val": 14, "auto_00001": [14, 19], "third": 14, "cannot": 14, "repeat": 14, "insert": [14, 33], "automat": [14, 19, 31], "manipul": [15, 17, 33], "grayscal": [15, 18], "morpholog": [15, 18], "quick": [15, 18], "t_": [15, 37], "text": [15, 17, 29, 37], "ro": [15, 37], "mechan": 15, "store": [15, 32, 37], "found": [15, 19, 33, 35, 37], "meta": 15, "05251": 15, "altern": [15, 37], "echo": [15, 29, 33, 34, 37], "ee": 15, "effectiveechospac": 15, "Then": [15, 37], "n_": 15, "rotim": 15, "00059": 15, "nonstandard": 15, "further": [15, 37], "confus": 15, "acceler": [15, 37], "grappa": 15, "arc": 15, "etc": [15, 33], "f_": 15, "acc": 15, "left": [15, 32, 33], "lfloor": 15, "frac": [15, 37], "right": [15, 16, 32], "rfloor": 15, "echospac": 15, "00119341": 15, "parallelreductionfactorinplan": 15, "philip": 15, "been": [15, 19, 33, 37], "quit": 15, "bit": 15, "engin": 15, "discuss": [15, 37], "around": [15, 18, 21, 33], "vendor": 15, "done": [15, 29, 33], "dr": 15, "rorden": 15, "summar": 15, "post": 15, "seem": 15, "wf": 15, "gamma": [15, 37], "delta_": [15, 17, 37], "w": [15, 33], "water": 15, "fat": 15, "strength": 15, "gyromagnet": [15, 37], "ratio": [15, 37], "ppm": 15, "plane": 15, "sens": 15, "absolut": [15, 18], "allow": [15, 19, 33], "train": 15, "length": 15, "size": [15, 25], "neither": 15, "acquisit": [15, 29, 34, 37], "strang": 15, "434": 15, "215": [15, 33], "earli": 15, "held": 15, "listserv": 15, "As": [15, 33, 35], "equival": [15, 29, 37], "frequenc": 15, "mhz": 15, "consol": 15, "prefer": 15, "accuraci": 15, "magnet": 15, "onc": 15, "waterfatshift": 15, "9": [15, 34, 35], "2227266": 15, "epifactor": 15, "35": 15, "imagingfrequ": 15, "127": [15, 33], "7325": 15, "5f": [15, 17], "magneticfieldstrength": 15, "enough": 15, "rais": 15, "hi": 15, "thorough": 15, "assess": 15, "matter": 15, "pravesh": 15, "parekh": 15, "wonder": 15, "review": 15, "neurostar": 15, "link": [15, 33, 37], "regard": 15, "voyag": 15, "pleas": [15, 33], "note": 15, "oe": 15, "believ": 15, "statement": 15, "about": [15, 33], "wrong": 15, "disappear": 15, "spinoza": 15, "guid": [15, 29], "preprocess": [15, 27, 29, 31, 32, 33, 34, 37], "basic": [16, 19], "miscellan": 16, "logger": [16, 19], "inlist": 16, "pop": 16, "otherwis": [16, 33], "untouch": 16, "somewher": 16, "probe": 16, "free": 16, "now": [16, 33], "newpath": 17, "arbitrari": [17, 18], "in_valu": 17, "te": [17, 29, 37], "echotime1": [17, 29], "00522": 17, "00768": 17, "00246": 17, "echotimediffer": 17, "in_refer": 18, "factor_tol": 18, "0001": 18, "cover": [18, 33], "whose": 18, "increas": [18, 33], "resolut": [18, 33], "extrem": [18, 33], "toler": [18, 33], "respect": 18, "la": 18, "source_ornt": 18, "target_ornt": 18, "natur": 18, "group": [18, 33], "ident": [18, 33], "thu": 18, "precomput": 18, "axcodes2ornt": 18, "psl": 18, "lp": 18, "air": [18, 29], "invert": 18, "ornt_transform": 18, "request": [18, 33], "anat_fil": 19, "bidsfil": 19, "layout": 19, "bidslayout": 19, "session": [19, 33, 37], "base_ent": 19, "anatom": [19, 26, 29, 31, 32, 33, 37], "pybid": [19, 33], "particip": [19, 27], "One": [19, 32, 37], "queri": [19, 33], "sbref": [19, 33], "place": 19, "diffus": [19, 37], "fmapless": [19, 37], "force_fmapless": [19, 37], "bids_filt": 19, "anat_suffix": 19, "heurist": [19, 33, 37], "less": [19, 27, 29, 30, 31, 33, 34], "_dwi": 19, "_bold": 19, "candid": [19, 37], "_t1w": 19, "complic": [19, 37], "_t2w": 19, "_sbref": 19, "manual": 19, "user": [19, 29, 33, 34], "suffic": 19, "skip": 19, "relai": 19, "messag": [19, 33], "lower": 19, "inclus": 19, "successfulli": 19, "built": [19, 37], "present": [19, 33], "ds000054": 19, "fmriprep": [19, 33], "magnitude1": [19, 33], "magnitude2": [19, 33], "100185": 19, "openneuro": 19, "four": 19, "ap": 19, "pa": [19, 33], "ds001771": [19, 33], "36": 19, "ds001600": 19, "test": [19, 33], "mani": [19, 37], "auto_00003": 19, "auto_00004": 19, "auto_00005": 19, "simplifi": [19, 33], "hcp": [19, 33], "purpos": [19, 26, 37], "hcp101006": 19, "101006": 19, "auto_00006": 19, "auto_00007": 19, "auto_00008": 19, "dsa": 19, "auto_": 19, "dsb": 19, "fm": 19, "likewis": 19, "comprehens": [19, 33], "veri": 19, "few": 19, "come": 19, "back": [19, 29, 33], "miss": [19, 33], "correctli": [19, 33], "investig": 19, "ds000206": 19, "05": [19, 34, 37], "dsc": 19, "pepolar4p": 19, "prioriti": 19, "opaque_perc": 21, "30": [21, 34], "transparent_perc": 21, "8": [21, 34], "coolwarm": 21, "color": 21, "scale": [21, 25, 29, 33], "transpar": [21, 33], "middl": 21, "anat_nii": 21, "div_id": 21, "plot_param": 21, "cut": 21, "estimate_bright": 21, "contour": 21, "compress": [21, 32], "auto": [21, 33], "overlai": 21, "overlay_param": 21, "plot": [21, 33], "foreground": [21, 33], "background": 21, "view": [21, 33], "axial": 21, "coron": 21, "sagitt": 21, "brainextraction_wf": 23, "nonbrain": 23, "tissu": 23, "bspline_dist": 23, "replac": [23, 33], "distanc": [23, 33], "separ": [23, 29, 33], "n4": [23, 29, 33], "smart": 23, "clip": [23, 37], "out_brain": 23, "probabl": 23, "random": 23, "walker": 23, "reach": 23, "soft": 23, "free_mem": 25, "omp_nthread": [25, 26, 27, 29, 30, 31], "unwarp_wf": [25, 33], "graph": [25, 26, 29, 30, 31], "png": [25, 26, 29, 30, 31], "pdf": [25, 26, 29, 30, 31], "individu": [25, 26, 27, 29, 37], "sloppi": [25, 26, 27, 29, 30, 31, 33], "fmap_coeff": [25, 26, 27, 29, 30, 31, 32], "hmc_xform": 25, "inhomogen": [25, 37], "fieldwarp": [25, 33], "appropri": [25, 33], "corrected_mask": 25, "fast": [25, 26, 29, 30, 31, 33, 37], "thereof": 26, "write_coeff": [26, 32], "coeff2epi_wf": 26, "trace": 26, "target_ref": 26, "target_mask": 26, "skull": [26, 29, 31, 37], "strip": [26, 29, 31, 37], "fmap_mask": [26, 29, 30, 32], "qualiti": 26, "target2fmap_xfm": 26, "style": 26, "produc": [26, 37], "antsapplytransform": [26, 37], "latter": 26, "output_dir": [27, 32], "fmap_preproc_wf": 27, "faster": 27, "precis": 27, "in_": 27, "depend": [27, 33, 34], "out_": 27, "measur": 29, "fmap_wf": 29, "mri": [29, 34, 37], "need": [29, 33], "surround": 29, "region": [29, 31, 37], "accur": [29, 30, 31, 33, 37], "short": [29, 30, 31], "descript": [29, 30, 31, 33, 35], "magnitude_wf": 29, "prepar": [29, 31, 33, 37], "part": [29, 34], "averag": [29, 31, 33, 37], "b1": 29, "nonuniform": 29, "phdiff_wf": 29, "consecut": 29, "besid": 29, "subtract": [29, 33], "core": 29, "reli": 29, "unwrap": [29, 33, 37], "prelud": 29, "jenkinson2003": [29, 37], "take": [29, 30, 37], "pi": [29, 37], "dotsb": [29, 37], "massag": [29, 33], "delta": [29, 37], "elsewher": 29, "subsequ": [29, 37], "pepolar_estimate_wf": 30, "afni": [30, 35, 37], "oppos": 30, "orthogon": 30, "task": [30, 31], "cpu": [30, 31, 33], "taken": 30, "convers": [30, 31, 33], "grid_refer": 30, "syn_preprocessing_wf": 31, "auto_bold_nss": 31, "t1w_invers": 31, "co": [31, 37], "nonsteadi": 31, "state": [31, 34], "detect": [31, 33], "intens": [31, 33, 37], "look": 31, "t2": 31, "merg": [31, 33], "togeth": [31, 33], "t_mask": 31, "Not": 31, "in_anat": 31, "t2w": [31, 33, 37], "mask_anat": 31, "std2anat_xfm": 31, "mni": 31, "templat": 31, "epi_ref": 31, "anat_ref": 31, "anat_mask": 31, "sd_prior": 31, "area": 31, "strong": 31, "sd": [31, 37], "cost": [31, 37], "atlas_threshold": 31, "syn_sdc_wf": 31, "restrict": [31, 33], "anterior": 31, "posterior": 31, "3mm": 31, "atla": [31, 33], "exclud": 31, "metric": 31, "below": [31, 37], "out_warp": [31, 33], "ref_mask": 31, "img_mask": 31, "histogram": [31, 37], "write": [32, 33], "allowed_ent": 32, "overload": 32, "source_fil": 32, "base_directori": 32, "check_hdr": 32, "fix": [32, 33, 37], "uncompress": 32, "unmodifi": 32, "data_dtyp": 32, "datatyp": 32, "coerc": 32, "tomatch": 32, "dismiss_ent": 32, "meta_dict": 32, "fixed_hdr": 32, "bids_fmap_id": 32, "custom_ent": 32, "fmap_derivatives_wf": 32, "datasink": 32, "defin": [32, 37], "written": [32, 35], "serv": 32, "fmap_typ": 32, "fmap_reports_wf": 32, "batteri": 32, "bug": 33, "lsqr": 33, "solver": 33, "rerun": 33, "366": 33, "367": 33, "rf": 33, "priorit": 33, "shortest": 33, "364": 33, "featur": 33, "behavior": 33, "addition": 33, "share": 33, "small": 33, "ux": 33, "themselv": 33, "360": 33, "enh": 33, "split": 33, "312": 33, "non": [33, 37], "358": 33, "355": 33, "356": 33, "intent": [33, 37], "342": 33, "ci": 33, "codecov": 33, "upload": 33, "348": 33, "inconsist": 33, "treatment": 33, "scanner": [33, 37], "were": [33, 37], "impact": 33, "354": 33, "captur": 33, "partial": 33, "351": 33, "incomplet": 33, "log": 33, "341": 33, "failur": 33, "343": 33, "nibabi": 33, "339": 33, "overli": 33, "335": 33, "334": 33, "squeez": 33, "simplebeforeaft": 33, "337": 33, "maint": 33, "circleci": 33, "secret": 33, "setup": 33, "org": 33, "329": 33, "326": 33, "switch": 33, "miniconda": 33, "instal": [33, 34], "conda": 33, "322": 33, "affect": 33, "324": 33, "doc": 33, "notebook": 33, "285": 33, "dynam": 33, "particularli": 33, "node": 33, "choos": 33, "constraint": 33, "321": 33, "thank": 33, "basil": 33, "pinsard": 33, "contribut": 33, "start": 33, "collat": 33, "317": 33, "319": 33, "coloc": 33, "308": 33, "scipi": 33, "311": 33, "pacifi": 33, "deprec": 33, "warn": 33, "stat": 33, "309": 33, "303": 33, "dens": 33, "wai": 33, "299": 33, "alter": 33, "basenam": 33, "293": 33, "287": 33, "288": 33, "coeff2epi": 33, "relat": 33, "278": 33, "4mm": 33, "re": 33, "314": 33, "n_proc": 33, "315": 33, "298": 33, "dure": 33, "292": 33, "304": 33, "integr": [33, 37], "downsampl": 33, "high": [33, 37], "301": 33, "284": 33, "usabl": 33, "257": 33, "robust": [33, 34, 37], "280": 33, "housekeep": 33, "302": 33, "gh": 33, "action": 33, "latest": 33, "282": 33, "keep": 33, "date": 33, "281": 33, "unavil": 33, "osf": 33, "remot": 33, "datalad": 33, "277": 33, "unus": 33, "276": 33, "concurr": 33, "permiss": 33, "313": 33, "roll": 33, "unittest": 33, "runner": 33, "ubuntu": 33, "310": 33, "trigger": 33, "weekli": 33, "270": 33, "incorpor": 33, "relax": 33, "concaten": 33, "265": 33, "minor": 33, "newest": 33, "niworkflow": 33, "distinct": 33, "261": 33, "mass": 33, "253": 33, "loosen": 33, "269": 33, "issu": 33, "21": 33, "next": 33, "262": 33, "intersphinx": 33, "url": 33, "263": 33, "258": 33, "docker": 33, "254": 33, "boilerpl": 33, "229": 33, "ishandl": 33, "higher": [33, 37], "251": 33, "b0field": 33, "bring": 33, "detail": [33, 37], "248": 33, "b0fieldsourc": 33, "247": 33, "deep": 33, "toward": 33, "overhaul": 33, "239": 33, "host": 33, "multivers": 33, "243": 33, "niprep": [33, 34], "240": [33, 37], "bugfix": 33, "discov": [33, 34], "237": 33, "228": 33, "234": 33, "page": 33, "push": 33, "histori": 33, "230": 33, "address": 33, "217": [33, 37], "expos": 33, "224": 33, "openpgp": 33, "sk": 33, "keyserv": 33, "223": 33, "hotfix": 33, "enhanc": [33, 37], "fine": 33, "tune": 33, "upstream": 33, "intensityclip": 33, "216": 33, "robustaverag": 33, "214": 33, "copyright": 33, "notic": 33, "comment": 33, "apach": 33, "212": 33, "uniform": [33, 37], "197": [33, 37], "210": 33, "209": 33, "hot": 33, "relev": 33, "inted": 33, "reliabl": 33, "api": [33, 34, 37], "advanc": 33, "nitranform": 33, "evad": 33, "fiddl": 33, "sure": [33, 35], "207": 33, "normal": [33, 37], "202": 33, "199": 33, "renam": 33, "182": 33, "180": 33, "204": 33, "191": 33, "188": 33, "pipelin": [33, 37], "184": 33, "rodent": 33, "inu": 33, "178": [33, 37], "adopt": 33, "176": 33, "typo": 33, "codespel": 33, "205": 33, "doubl": 33, "200": 33, "divid": [33, 37], "ambigu": 33, "smaller": 33, "focus": 33, "190": 33, "github": 33, "upgrad": 33, "185": 33, "minim": [33, 34], "major": [33, 37], "softwar": [33, 35, 37], "vision": 33, "subordin": 33, "inlin": 33, "smriprep": 33, "idea": 33, "consid": 33, "citizen": 33, "vein": 33, "ey": 33, "suffici": 33, "under": 33, "suit": [33, 37], "dmriprep": 33, "exercis": 33, "artifact": [33, 37], "popul": 33, "piec": 33, "forward": 33, "leverag": 33, "choic": 33, "boldref": 33, "accordingli": 33, "coverag": 33, "cleanup": 33, "promin": [33, 37], "pull": 33, "conduc": 33, "bet": 33, "174": 33, "svgutil": 33, "break": 33, "175": 33, "misconfigur": 33, "170": 33, "annoi": 33, "isol": 33, "dot": 33, "168": 33, "afterward": 33, "165": 33, "sei": [33, 37], "stabil": 33, "128": 33, "166": 33, "164": 33, "simpl": 33, "161": 33, "159": 33, "157": 33, "blocksiz": 33, "156": 33, "154": 33, "simplist": 33, "152": 33, "151": 33, "fmapid": 33, "150": 33, "multiplex": 33, "outputnod": 33, "149": 33, "put": 33, "143": 33, "autogener": 33, "142": 33, "132": 33, "130": 33, "114": 33, "120": 33, "115": 33, "liter": 33, "162": 33, "155": 33, "sphinx": 33, "extens": 33, "render": 33, "131": 33, "makefil": 33, "173": 33, "retouch": 33, "sever": [33, 37], "172": 33, "160": 33, "git": 33, "archiv": 33, "protocol": [33, 34, 37], "setuptool": 33, "scm": 33, "153": 33, "migrat": 33, "travisci": 33, "complet": 33, "138": 33, "137": 33, "refactor": 33, "133": 33, "circl": 33, "122": 33, "96": 33, "flirt": 33, "config": 33, "116": 33, "repo": 33, "contributor": 33, "guidelin": 33, "anyon": 33, "develop": [33, 34, 37], "manuscript": 33, "markiewicz": 33, "christoph": 33, "goncalv": 33, "mathia": 33, "macnicol": 33, "eilidh": 33, "adebimp": 33, "azeez": 33, "blair": 33, "ross": 33, "cieslak": 33, "matthew": 33, "naveau": 33, "mika\u00ebl": 33, "sitek": 33, "kevin": 33, "r": [33, 37], "sneve": 33, "marku": 33, "h": [33, 37], "gorgolewski": 33, "krzysztof": 33, "satterthwait": 33, "theodor": 33, "poldrack": 33, "russel": 33, "esteban": [33, 37], "oscar": 33, "affili": 33, "depart": 33, "psychologi": 33, "stanford": 33, "univers": 33, "neuroimag": [33, 34, 35, 37], "king": 33, "colleg": 33, "london": 33, "perelman": 33, "school": 33, "medicin": 33, "pennsylvania": 33, "usa": 33, "cyceron": 33, "um": 33, "3408": 33, "cnr": 33, "ucbn": 33, "franc": 33, "speech": 33, "hear": 33, "bioscienc": 33, "technologi": 33, "harvard": 33, "lifespan": 33, "cognit": 33, "oslo": 33, "dept": 33, "radiologi": 33, "lausann": 33, "hospit": 33, "371": 33, "machin": 33, "branch": 33, "327": 33, "nan": 33, "104": 33, "108": 33, "newli": 33, "refacor": 33, "102": 33, "enforc": 33, "dseg": 33, "wm": 33, "select": 33, "100": 33, "98": 33, "amic": 33, "downstream": 33, "setuptools_scm": 33, "97": 33, "flexibil": 33, "95": 33, "caclul": 33, "2pi": 33, "88": 33, "mnt": 33, "90": 33, "deploy": 33, "91": 33, "nomin": 33, "central": 33, "outlier": 33, "89": 33, "connect": 33, "whenev": 33, "82": 33, "skim": 33, "80": 33, "prevent": 33, "collis": 33, "pin": 33, "449c2c2": 33, "intramodalmerg": 33, "choke": 33, "79": 33, "2e6faa0": 33, "717a69": 33, "361cd67": 33, "flexibli": 33, "cheapli": 33, "75": 33, "70": 33, "stabl": 33, "detach": 33, "off": 33, "hard": 33, "wire": 33, "mni152nlin2009casym": 33, "63": 33, "60": 33, "get_data": 33, "get_fdata": 33, "58": 33, "flow": 33, "homogen": 33, "56": 33, "57": 33, "stop": 33, "siemens2rad": 33, "old": 33, "orchestr": 33, "55": 33, "53": 33, "dedupl": 33, "postprocess": 33, "52": [33, 37], "legaci": [33, 37], "51": 33, "61": 33, "49": [33, 37], "43": 33, "fork": 33, "48": 33, "refresh": 33, "workdir": 33, "commit": 33, "47": 33, "local": 33, "45": 33, "flake8": 33, "44": 33, "distortedref": 33, "41": 33, "niflow": 33, "nipype1": 33, "39": 33, "mainten": 33, "0rc1": 33, "bad": 33, "NOT": 33, "fixup": 33, "deploi": [33, 35], "infrastructur": 33, "manifest": 33, "effigi": 33, "work": 33, "v1": 33, "librari": 34, "displai": 34, "acquir": [34, 37], "planar": [34, 37], "mr": [34, 37], "scheme": [34, 37], "art": 34, "open": 34, "being": 34, "analysi": [34, 37], "reproduc": 34, "platform": 34, "offer": 34, "extern": 34, "theori": 34, "techniqu": 34, "unsupport": 34, "implicit": 34, "t1": 34, "applic": [34, 37], "what": 34, "june": 34, "08": [34, 37], "2023": 34, "april": 34, "24": 34, "march": 34, "10": [34, 37], "januari": 34, "04": 34, "decemb": 34, "2022": 34, "09": 34, "august": 34, "29": 34, "26": 34, "13": 34, "februari": 34, "11": [34, 37], "2021": 34, "novemb": 34, "octob": 34, "15": 34, "septemb": 34, "18": 34, "14": 34, "25": 34, "juli": 34, "07": [34, 35], "2020": 34, "pre": [34, 37], "releas": 34, "27": 34, "2019": 34, "23": 34, "dockerfil": 35, "freesurf": 35, "licens": 35, "pip": 35, "habitu": 35, "__version__": 35, "pypi": 35, "neurodock": 35, "debian": 35, "behind": 37, "literatur": 37, "jezzard1995": 37, "hutton2002": 37, "summari": 37, "fig": 37, "freeli": 37, "three": 37, "proport": 37, "nutshel": 37, "suffer": 37, "proton": 37, "42": 37, "576": 37, "variat": 37, "tesla": 37, "let": 37, "veloc": 37, "s_": 37, "nonzero": 37, "compon": 37, "d_": 37, "drift": 37, "least": 37, "via": 37, "theta": 37, "elaps": 37, "simplic": 37, "fact": 37, "theta_i": 37, "offset": 37, "continu": 37, "neighbor": 37, "exploit": 37, "symmetri": 37, "andersson2003": 37, "cox1997": 37, "studi": 37, "especi": 37, "absenc": 37, "research": 37, "resort": 37, "nonlinear": 37, "propos": 37, "studholme2000": 37, "experiment": 37, "procedur": 37, "symmetr": 37, "treiber2016": 37, "huntenburg2014": 37, "wang2017": 37, "Such": 37, "aid": 37, "matt": 37, "laplacian": 37, "gradient": 37, "folder": 37, "outcom": 37, "scrutin": 37, "caution": 37, "feedback": 37, "enthusiast": 37, "There": 37, "spread": 37, "zaitsev2004": 37, "surfac": 37, "esteban2016": 37, "cornerston": 37, "plausibli": 37, "fewer": 37, "eas": 37, "try": 37, "workabl": 37, "shim": 37, "jezzard": 37, "balaban": 37, "1995": 37, "geometr": 37, "magn": 37, "reson": 37, "med": 37, "34": 37, "65": 37, "73": 37, "doi": 37, "1002": 37, "mrm": 37, "1910340111": 37, "hutton": 37, "2002": 37, "fmri": 37, "quantit": 37, "1006": 37, "nimg": 37, "2001": 37, "1054": 37, "jenkinson": 37, "2003": 37, "193": 37, "10354": 37, "andersson": 37, "spin": 37, "870": 37, "888": 37, "1016": 37, "s1053": 37, "8119": 37, "03": 37, "00336": 37, "cox": 37, "1997": 37, "nmr": 37, "biom": 37, "171": 37, "sici": 37, "1099": 37, "1492": 37, "199706": 37, "3c171": 37, "nbm453": 37, "3e3": 37, "l": 37, "studholm": 37, "2000": 37, "tran": 37, "19": 37, "1115": 37, "1127": 37, "1109": 37, "896788": 37, "treiber": 37, "2016": 37, "character": 37, "814": 37, "plo": 37, "ONE": 37, "e0152472": 37, "1371": 37, "journal": 37, "pone": 37, "0152472": 37, "wang": 37, "2017": 37, "neuroinform": 37, "3389": 37, "fninf": 37, "00017": 37, "huntenburg": 37, "2014": 37, "coregistr": 37, "berlin": 37, "master": 37, "thesi": 37, "freie": 37, "universit\u00e4t": 37, "zaitsev": 37, "2004": 37, "1156": 37, "1166": 37, "20261": 37, "driven": 37, "139": 37, "450": 37, "461": 37, "011": 37}, "objects": {"sdcflows": [[1, 0, 0, "-", "cli"], [3, 0, 0, "-", "data"], [4, 0, 0, "-", "fieldmaps"], [5, 0, 0, "-", "interfaces"], [12, 0, 0, "-", "transform"], [13, 0, 0, "-", "utils"], [20, 0, 0, "-", "viz"], [22, 0, 0, "-", "workflows"]], "sdcflows.cli": [[2, 0, 0, "-", "find_estimators"]], "sdcflows.cli.find_estimators": [[2, 1, 1, "", "gen_layout"], [2, 1, 1, "", "main"]], "sdcflows.data": [[3, 2, 1, "", "Loader"], [3, 1, 1, "", "load"]], "sdcflows.data.Loader": [[3, 3, 1, "", "as_path"], [3, 3, 1, "", "cached"], [3, 3, 1, "", "readable"]], "sdcflows.data.load": [[3, 3, 1, "", "as_path"], [3, 3, 1, "", "cached"], [3, 3, 1, "", "readable"]], "sdcflows.fieldmaps": [[4, 2, 1, "", "EstimatorType"], [4, 2, 1, "", "FieldmapEstimation"], [4, 2, 1, "", "FieldmapFile"], [4, 5, 1, "", "MetadataError"], [4, 1, 1, "", "clear_registry"], [4, 1, 1, "", "get_identifier"]], "sdcflows.fieldmaps.EstimatorType": [[4, 4, 1, "", "ANAT"], [4, 4, 1, "", "MAPPED"], [4, 4, 1, "", "PEPOLAR"], [4, 4, 1, "", "PHASEDIFF"], [4, 4, 1, "", "UNKNOWN"]], "sdcflows.fieldmaps.FieldmapEstimation": [[4, 4, 1, "", "bids_id"], [4, 3, 1, "", "get_workflow"], [4, 4, 1, "", "method"], [4, 3, 1, "", "paths"], [4, 4, 1, "", "sources"]], "sdcflows.fieldmaps.FieldmapFile": [[4, 4, 1, "", "bids_root"], [4, 3, 1, "", "check_path"], [4, 4, 1, "", "entities"], [4, 4, 1, "", "find_meta"], [4, 4, 1, "", "metadata"], [4, 4, 1, "", "path"], [4, 4, 1, "", "suffix"]], "sdcflows.interfaces": [[6, 0, 0, "-", "brainmask"], [7, 0, 0, "-", "bspline"], [8, 0, 0, "-", "epi"], [9, 0, 0, "-", "fmap"], [10, 0, 0, "-", "reportlets"], [11, 0, 0, "-", "utils"]], "sdcflows.interfaces.brainmask": [[6, 2, 1, "", "BinaryDilation"], [6, 2, 1, "", "BrainExtraction"], [6, 2, 1, "", "Union"]], "sdcflows.interfaces.bspline": [[7, 2, 1, "", "ApplyCoeffsField"], [7, 2, 1, "", "BSplineApprox"], [7, 2, 1, "", "TOPUPCoeffReorient"], [7, 2, 1, "", "TransformCoefficients"], [7, 1, 1, "", "bspline_grid"]], "sdcflows.interfaces.epi": [[8, 2, 1, "", "GetReadoutTime"], [8, 2, 1, "", "SortPEBlips"]], "sdcflows.interfaces.fmap": [[9, 2, 1, "", "CheckB0Units"], [9, 2, 1, "", "CheckRegister"], [9, 2, 1, "", "DisplacementsField2Fieldmap"], [9, 2, 1, "", "PhaseMap2rads"], [9, 2, 1, "", "Phasediff2Fieldmap"], [9, 2, 1, "", "SubtractPhases"]], "sdcflows.interfaces.reportlets": [[10, 2, 1, "", "FieldmapReportlet"]], "sdcflows.interfaces.utils": [[11, 2, 1, "", "ConvertWarp"], [11, 2, 1, "", "DenoiseImage"], [11, 2, 1, "", "Deoblique"], [11, 2, 1, "", "Flatten"], [11, 2, 1, "", "PadSlices"], [11, 2, 1, "", "PositiveDirectionCosines"], [11, 2, 1, "", "Reoblique"], [11, 2, 1, "", "ReorientImageAndMetadata"], [11, 2, 1, "", "UniformGrid"]], "sdcflows.transform": [[12, 2, 1, "", "B0FieldTransform"], [12, 1, 1, "", "disp_to_fmap"], [12, 1, 1, "", "fmap_to_disp"], [12, 1, 1, "", "grid_bspline_weights"], [12, 1, 1, "", "unwarp_parallel"], [12, 1, 1, "", "worker"]], "sdcflows.transform.B0FieldTransform": [[12, 3, 1, "", "apply"], [12, 4, 1, "", "coeffs"], [12, 3, 1, "", "fit"], [12, 4, 1, "", "mapped"], [12, 3, 1, "", "to_displacements"]], "sdcflows.utils": [[14, 0, 0, "-", "bimap"], [15, 0, 0, "-", "epimanip"], [16, 0, 0, "-", "misc"], [17, 0, 0, "-", "phasemanip"], [18, 0, 0, "-", "tools"], [19, 0, 0, "-", "wrangler"]], "sdcflows.utils.bimap": [[14, 2, 1, "", "EstimatorRegistry"], [14, 2, 1, "", "bidict"]], "sdcflows.utils.bimap.EstimatorRegistry": [[14, 3, 1, "", "get_key"], [14, 6, 1, "", "sources"]], "sdcflows.utils.bimap.bidict": [[14, 3, 1, "", "add"], [14, 3, 1, "", "clear"]], "sdcflows.utils.epimanip": [[15, 1, 1, "", "epi_mask"], [15, 1, 1, "", "get_trt"]], "sdcflows.utils.misc": [[16, 1, 1, "", "create_logger"], [16, 1, 1, "", "front"], [16, 1, 1, "", "get_free_mem"], [16, 1, 1, "", "last"]], "sdcflows.utils.phasemanip": [[17, 1, 1, "", "au2rads"], [17, 1, 1, "", "delta_te"], [17, 1, 1, "", "phdiff2fmap"], [17, 1, 1, "", "subtract_phases"]], "sdcflows.utils.tools": [[18, 1, 1, "", "brain_masker"], [18, 1, 1, "", "deoblique_and_zooms"], [18, 1, 1, "", "ensure_positive_cosines"], [18, 1, 1, "", "reorient_pedir"], [18, 1, 1, "", "resample_to_zooms"]], "sdcflows.utils.wrangler": [[19, 1, 1, "", "find_anatomical_estimators"], [19, 1, 1, "", "find_estimators"]], "sdcflows.viz": [[21, 0, 0, "-", "utils"]], "sdcflows.viz.utils": [[21, 1, 1, "", "coolwarm_transparent"], [21, 1, 1, "", "plot_registration"]], "sdcflows.workflows": [[23, 0, 0, "-", "ancillary"], [24, 0, 0, "-", "apply"], [27, 0, 0, "-", "base"], [28, 0, 0, "-", "fit"], [32, 0, 0, "-", "outputs"]], "sdcflows.workflows.ancillary": [[23, 1, 1, "", "init_brainextraction_wf"]], "sdcflows.workflows.apply": [[25, 0, 0, "-", "correction"], [26, 0, 0, "-", "registration"]], "sdcflows.workflows.apply.correction": [[25, 1, 1, "", "init_unwarp_wf"]], "sdcflows.workflows.apply.registration": [[26, 1, 1, "", "init_coeff2epi_wf"]], "sdcflows.workflows.base": [[27, 1, 1, "", "init_fmap_preproc_wf"]], "sdcflows.workflows.fit": [[29, 0, 0, "-", "fieldmap"], [30, 0, 0, "-", "pepolar"], [31, 0, 0, "-", "syn"]], "sdcflows.workflows.fit.fieldmap": [[29, 1, 1, "", "init_fmap_wf"], [29, 1, 1, "", "init_magnitude_wf"], [29, 1, 1, "", "init_phdiff_wf"]], "sdcflows.workflows.fit.pepolar": [[30, 1, 1, "", "init_3dQwarp_wf"], [30, 1, 1, "", "init_topup_wf"]], "sdcflows.workflows.fit.syn": [[31, 1, 1, "", "init_syn_preprocessing_wf"], [31, 1, 1, "", "init_syn_sdc_wf"], [31, 1, 1, "", "match_histogram"]], "sdcflows.workflows.outputs": [[32, 2, 1, "", "DerivativesDataSink"], [32, 1, 1, "", "init_fmap_derivatives_wf"], [32, 1, 1, "", "init_fmap_reports_wf"]], "sdcflows.workflows.outputs.DerivativesDataSink": [[32, 4, 1, "", "out_path_base"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method", "4": "py:attribute", "5": "py:exception", "6": "py:property"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "exception", "Python exception"], "6": ["py", "property", "Python property"]}, "titleterms": {"librari": 0, "api": 0, "applic": 0, "program": 0, "interfac": [0, 5, 6, 7, 8, 9, 10, 11], "sdcflow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], "cli": [1, 2], "packag": [1, 3, 5, 13, 20, 22, 24, 28], "submodul": [1, 5, 13, 20, 22, 24, 28], "find_estim": 2, "modul": [2, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 29, 30, 31, 32], "data": [3, 37], "fieldmap": [4, 29, 37], "brainmask": 6, "bspline": 7, "epi": 8, "fmap": 9, "reportlet": 10, "util": [11, 13, 14, 15, 16, 17, 18, 19, 21], "transform": 12, "bimap": 14, "epimanip": 15, "thank": 15, "see": 15, "also": 15, "misc": 16, "phasemanip": 17, "tool": [18, 37], "wrangler": 19, "viz": [20, 21], "workflow": [22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "subpackag": 22, "ancillari": 23, "appli": [24, 25, 26], "correct": 25, "registr": [26, 37], "base": [27, 33], "fit": [28, 29, 30, 31], "pepolar": [30, 37], "syn": 31, "output": 32, "what": 33, "": 33, "new": 33, "2": 33, "5": 33, "1": 33, "june": 33, "08": 33, "2023": 33, "0": 33, "01": 33, "4": 33, "3": 33, "april": 33, "24": 33, "20": 33, "march": 33, "10": 33, "januari": 33, "04": 33, "decemb": 33, "12": 33, "2022": 33, "09": 33, "august": 33, "29": 33, "mai": 33, "26": 33, "13": 33, "februari": 33, "11": 33, "22": 33, "2021": 33, "9": 33, "novemb": 33, "16": 33, "8": 33, "octob": 33, "15": 33, "7": 33, "septemb": 33, "30": 33, "6": 33, "18": 33, "14": 33, "05": 33, "25": 33, "author": 33, "list": 33, "paper": 33, "x": 33, "seri": 33, "juli": 33, "07": 33, "2020": 33, "pre": 33, "releas": 33, "27": 33, "2019": 33, "23": 33, "content": 34, "instal": 35, "extern": 35, "depend": 35, "method": 37, "implement": 37, "bid": 37, "specif": 37, "estim": 37, "theori": 37, "direct": 37, "b0": 37, "map": 37, "sequenc": 37, "phase": 37, "differ": 37, "techniqu": 37, "less": 37, "approach": 37, "other": 37, "unsupport": 37, "unwarp": 37, "distort": 37, "discov": 37, "dataset": 37, "explicit": 37, "b0fieldidentifi": 37, "implicit": 37, "intendedfor": 37, "t1": 37, "weight": 37, "imag": 37, "refer": 37}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Library API (application program interface)": [[0, "library-api-application-program-interface"]], "sdcflows.cli package": [[1, "module-sdcflows.cli"]], "Submodules": [[1, "submodules"], [5, "submodules"], [13, "submodules"], [20, "submodules"], [22, "submodules"], [24, "submodules"], [28, "submodules"]], "sdcflows.cli.find_estimators module": [[2, "module-sdcflows.cli.find_estimators"]], "sdcflows.data package": [[3, "module-sdcflows.data"]], "sdcflows.fieldmaps module": [[4, "module-sdcflows.fieldmaps"]], "sdcflows.interfaces package": [[5, "module-sdcflows.interfaces"]], "sdcflows.interfaces.brainmask module": [[6, "module-sdcflows.interfaces.brainmask"]], "sdcflows.interfaces.bspline module": [[7, "module-sdcflows.interfaces.bspline"]], "sdcflows.interfaces.epi module": [[8, "module-sdcflows.interfaces.epi"]], "sdcflows.interfaces.fmap module": [[9, "module-sdcflows.interfaces.fmap"]], "sdcflows.interfaces.reportlets module": [[10, "module-sdcflows.interfaces.reportlets"]], "sdcflows.interfaces.utils module": [[11, "module-sdcflows.interfaces.utils"]], "sdcflows.transform module": [[12, "module-sdcflows.transform"]], "sdcflows.utils package": [[13, "module-sdcflows.utils"]], "sdcflows.utils.bimap module": [[14, "module-sdcflows.utils.bimap"]], "sdcflows.utils.epimanip module": [[15, "module-sdcflows.utils.epimanip"]], "Thanks": [[15, null]], "See Also": [[15, null]], "sdcflows.utils.misc module": [[16, "module-sdcflows.utils.misc"]], "sdcflows.utils.phasemanip module": [[17, "module-sdcflows.utils.phasemanip"]], "sdcflows.utils.tools module": [[18, "module-sdcflows.utils.tools"]], "sdcflows.utils.wrangler module": [[19, "module-sdcflows.utils.wrangler"]], "sdcflows.viz package": [[20, "module-sdcflows.viz"]], "sdcflows.viz.utils module": [[21, "module-sdcflows.viz.utils"]], "sdcflows.workflows package": [[22, "module-sdcflows.workflows"]], "Subpackages": [[22, "subpackages"]], "sdcflows.workflows.ancillary module": [[23, "module-sdcflows.workflows.ancillary"]], "sdcflows.workflows.apply package": [[24, "module-sdcflows.workflows.apply"]], "sdcflows.workflows.apply.correction module": [[25, "module-sdcflows.workflows.apply.correction"]], "sdcflows.workflows.apply.registration module": [[26, "module-sdcflows.workflows.apply.registration"]], "sdcflows.workflows.base module": [[27, "module-sdcflows.workflows.base"]], "sdcflows.workflows.fit package": [[28, "module-sdcflows.workflows.fit"]], "sdcflows.workflows.fit.fieldmap module": [[29, "module-sdcflows.workflows.fit.fieldmap"]], "sdcflows.workflows.fit.pepolar module": [[30, "module-sdcflows.workflows.fit.pepolar"]], "sdcflows.workflows.fit.syn module": [[31, "module-sdcflows.workflows.fit.syn"]], "sdcflows.workflows.outputs module": [[32, "module-sdcflows.workflows.outputs"]], "What\u2019s new?": [[33, "what-s-new"]], "2.5.1 (June 08, 2023)": [[33, "june-08-2023"]], "2.5.0 (June 01, 2023)": [[33, "june-01-2023"]], "2.4.3 (April 24, 2023)": [[33, "april-24-2023"]], "2.4.2 (April 20, 2023)": [[33, "april-20-2023"]], "2.4.1 (March 20, 2023)": [[33, "march-20-2023"]], "2.4.0 (March 10, 2023)": [[33, "march-10-2023"]], "2.3.0 (March 01, 2023)": [[33, "march-01-2023"]], "2.2.2 (January 04, 2023)": [[33, "january-04-2023"]], "2.2.1 (December 12, 2022)": [[33, "december-12-2022"]], "2.2.0 (December 09, 2022)": [[33, "december-09-2022"]], "2.1.1 (August 29, 2022)": [[33, "august-29-2022"]], "2.1.0 (May 26, 2022)": [[33, "may-26-2022"]], "2.0.13 (April 08, 2022)": [[33, "april-08-2022"]], "2.0.12 (February 08, 2022)": [[33, "february-08-2022"]], "2.0.11 (January 22, 2022)": [[33, "january-22-2022"]], "2.0.10 (December 13, 2021)": [[33, "december-13-2021"]], "2.0.9 (November 16, 2021)": [[33, "november-16-2021"]], "2.0.8 (October 15, 2021)": [[33, "october-15-2021"]], "2.0.7 (September 30, 2021)": [[33, "september-30-2021"]], "2.0.6 (September 1, 2021)": [[33, "september-1-2021"]], "2.0.5 (August 24, 2021)": [[33, "august-24-2021"]], "2.0.4 (May 18, 2021)": [[33, "may-18-2021"]], "2.0.3 (May 14, 2021)": [[33, "may-14-2021"]], "2.0.2 (May 11, 2021)": [[33, "may-11-2021"]], "2.0.1 (March 05, 2021)": [[33, "march-05-2021"]], "2.0.0 (January 25, 2021)": [[33, "january-25-2021"]], "Author list for papers based on SDCFlows 2.0.x series": [[33, null]], "1.3.x series": [[33, "x-series"]], "1.3.4 (July 07, 2023)": [[33, "july-07-2023"]], "1.3.3 (September 4, 2020)": [[33, "september-4-2020"]], "1.3.2 (August 14, 2020)": [[33, "august-14-2020"]], "1.3.1 (May 22, 2020)": [[33, "may-22-2020"]], "1.3.0 (May 4, 2020)": [[33, "may-4-2020"]], "Pre-1.3.x releases": [[33, "pre-1-3-x-releases"]], "1.2.2 (April 16, 2020)": [[33, "april-16-2020"]], "1.2.1 (April 01, 2020)": [[33, "april-01-2020"]], "1.2.0 (February 15, 2020)": [[33, "february-15-2020"]], "1.1.0 (February 3, 2020)": [[33, "february-3-2020"]], "1.0.6 (April 15, 2020)": [[33, "april-15-2020"]], "1.0.5 (February 14, 2020)": [[33, "february-14-2020"]], "1.0.4 (January 27, 2020)": [[33, "january-27-2020"]], "1.0.3 (December 18, 2019)": [[33, "december-18-2019"]], "1.0.2 (December 18, 2019)": [[33, "id1"]], "1.0.1 (December 04, 2019)": [[33, "december-04-2019"]], "1.0.0 (November 25, 2019)": [[33, "november-25-2019"]], "0.1.4 (November 22, 2019)": [[33, "november-22-2019"]], "0.1.3 (October 15, 2019)": [[33, "october-15-2019"]], "0.1.2 (October 10, 2019)": [[33, "october-10-2019"]], "0.1.1 (July 23, 2019)": [[33, "july-23-2019"]], "0.1.0 (July 22, 2019)": [[33, "july-22-2019"]], "SDCFlows": [[34, "sdcflows"]], "Contents": [[34, "contents"]], "Installation": [[35, "id1"]], "External Dependencies": [[35, "external-dependencies"]], "Methods and implementation": [[37, "methods-and-implementation"]], "BIDS Specification": [[37, null], [37, null], [37, null], [37, null], [37, null], [37, null]], "Fieldmap estimation: theory and methods": [[37, "fieldmap-estimation-theory-and-methods"]], "Direct B0 mapping sequences": [[37, "direct-b0-mapping-sequences"]], "Phase-difference B0 estimation": [[37, "phase-difference-b0-estimation"]], "PEPOLAR techniques": [[37, "pepolar-techniques"]], "Fieldmap-less approaches": [[37, "fieldmap-less-approaches"]], "Other (unsupported) approaches": [[37, "other-unsupported-approaches"]], "Estimation tooling": [[37, "estimation-tooling"]], "Unwarping the distorted data": [[37, "unwarping-the-distorted-data"]], "Discovering fieldmaps in a BIDS dataset": [[37, "discovering-fieldmaps-in-a-bids-dataset"]], "Explicit specification with B0FieldIdentifier": [[37, "explicit-specification-with-b0fieldidentifier"]], "Implicit specification with IntendedFor": [[37, "implicit-specification-with-intendedfor"]], "Fieldmap-less by registration to a T1-weighted image": [[37, "fieldmap-less-by-registration-to-a-t1-weighted-image"]], "References": [[37, "references"]]}, "indexentries": {"module": [[1, "module-sdcflows.cli"], [2, "module-sdcflows.cli.find_estimators"], [3, "module-sdcflows.data"], [4, "module-sdcflows.fieldmaps"], [5, "module-sdcflows.interfaces"], [6, "module-sdcflows.interfaces.brainmask"], [7, "module-sdcflows.interfaces.bspline"], [8, "module-sdcflows.interfaces.epi"], [9, "module-sdcflows.interfaces.fmap"], [10, "module-sdcflows.interfaces.reportlets"], [11, "module-sdcflows.interfaces.utils"], [12, "module-sdcflows.transform"], [13, "module-sdcflows.utils"], [14, "module-sdcflows.utils.bimap"], [15, "module-sdcflows.utils.epimanip"], [16, "module-sdcflows.utils.misc"], [17, "module-sdcflows.utils.phasemanip"], [18, "module-sdcflows.utils.tools"], [19, "module-sdcflows.utils.wrangler"], [20, "module-sdcflows.viz"], [21, "module-sdcflows.viz.utils"], [22, "module-sdcflows.workflows"], [23, "module-sdcflows.workflows.ancillary"], [24, "module-sdcflows.workflows.apply"], [25, "module-sdcflows.workflows.apply.correction"], [26, "module-sdcflows.workflows.apply.registration"], [27, "module-sdcflows.workflows.base"], [28, "module-sdcflows.workflows.fit"], [29, "module-sdcflows.workflows.fit.fieldmap"], [30, "module-sdcflows.workflows.fit.pepolar"], [31, "module-sdcflows.workflows.fit.syn"], [32, "module-sdcflows.workflows.outputs"]], "sdcflows.cli": [[1, "module-sdcflows.cli"]], "gen_layout() (in module sdcflows.cli.find_estimators)": [[2, "sdcflows.cli.find_estimators.gen_layout"]], "main() (in module sdcflows.cli.find_estimators)": [[2, "sdcflows.cli.find_estimators.main"]], "sdcflows.cli.find_estimators": [[2, "module-sdcflows.cli.find_estimators"]], "loader (class in sdcflows.data)": [[3, "sdcflows.data.Loader"]], "as_path() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.as_path"]], "as_path() (sdcflows.data.load method)": [[3, "sdcflows.data.load.as_path"]], "cached() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.cached"]], "cached() (sdcflows.data.load method)": [[3, "sdcflows.data.load.cached"]], "load() (in module sdcflows.data)": [[3, "sdcflows.data.load"]], "readable() (sdcflows.data.loader method)": [[3, "sdcflows.data.Loader.readable"]], "readable() (sdcflows.data.load method)": [[3, "sdcflows.data.load.readable"]], "sdcflows.data": [[3, "module-sdcflows.data"]], "anat (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.ANAT"]], "estimatortype (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.EstimatorType"]], "fieldmapestimation (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.FieldmapEstimation"]], "fieldmapfile (class in sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.FieldmapFile"]], "mapped (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.MAPPED"]], "metadataerror": [[4, "sdcflows.fieldmaps.MetadataError"]], "pepolar (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.PEPOLAR"]], "phasediff (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.PHASEDIFF"]], "unknown (sdcflows.fieldmaps.estimatortype attribute)": [[4, "sdcflows.fieldmaps.EstimatorType.UNKNOWN"]], "bids_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.bids_id"]], "bids_root (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.bids_root"]], "check_path() (sdcflows.fieldmaps.fieldmapfile method)": [[4, "sdcflows.fieldmaps.FieldmapFile.check_path"]], "clear_registry() (in module sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.clear_registry"]], "entities (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.entities"]], "find_meta (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.find_meta"]], "get_identifier() (in module sdcflows.fieldmaps)": [[4, "sdcflows.fieldmaps.get_identifier"]], "get_workflow() (sdcflows.fieldmaps.fieldmapestimation method)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.get_workflow"]], "metadata (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.metadata"]], "method (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.method"]], "path (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.path"]], "paths() (sdcflows.fieldmaps.fieldmapestimation method)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.paths"]], "sdcflows.fieldmaps": [[4, "module-sdcflows.fieldmaps"]], "sources (sdcflows.fieldmaps.fieldmapestimation attribute)": [[4, "sdcflows.fieldmaps.FieldmapEstimation.sources"]], "suffix (sdcflows.fieldmaps.fieldmapfile attribute)": [[4, "sdcflows.fieldmaps.FieldmapFile.suffix"]], "sdcflows.interfaces": [[5, "module-sdcflows.interfaces"]], "binarydilation (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.BinaryDilation"]], "brainextraction (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.BrainExtraction"]], "union (class in sdcflows.interfaces.brainmask)": [[6, "sdcflows.interfaces.brainmask.Union"]], "sdcflows.interfaces.brainmask": [[6, "module-sdcflows.interfaces.brainmask"]], "applycoeffsfield (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.ApplyCoeffsField"]], "bsplineapprox (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.BSplineApprox"]], "topupcoeffreorient (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.TOPUPCoeffReorient"]], "transformcoefficients (class in sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.TransformCoefficients"]], "bspline_grid() (in module sdcflows.interfaces.bspline)": [[7, "sdcflows.interfaces.bspline.bspline_grid"]], "sdcflows.interfaces.bspline": [[7, "module-sdcflows.interfaces.bspline"]], "getreadouttime (class in sdcflows.interfaces.epi)": [[8, "sdcflows.interfaces.epi.GetReadoutTime"]], "sortpeblips (class in sdcflows.interfaces.epi)": [[8, "sdcflows.interfaces.epi.SortPEBlips"]], "sdcflows.interfaces.epi": [[8, "module-sdcflows.interfaces.epi"]], "checkb0units (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.CheckB0Units"]], "checkregister (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.CheckRegister"]], "displacementsfield2fieldmap (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.DisplacementsField2Fieldmap"]], "phasemap2rads (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.PhaseMap2rads"]], "phasediff2fieldmap (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.Phasediff2Fieldmap"]], "subtractphases (class in sdcflows.interfaces.fmap)": [[9, "sdcflows.interfaces.fmap.SubtractPhases"]], "sdcflows.interfaces.fmap": [[9, "module-sdcflows.interfaces.fmap"]], "fieldmapreportlet (class in sdcflows.interfaces.reportlets)": [[10, "sdcflows.interfaces.reportlets.FieldmapReportlet"]], "sdcflows.interfaces.reportlets": [[10, "module-sdcflows.interfaces.reportlets"]], "convertwarp (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.ConvertWarp"]], "denoiseimage (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.DenoiseImage"]], "deoblique (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Deoblique"]], "flatten (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Flatten"]], "padslices (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.PadSlices"]], "positivedirectioncosines (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.PositiveDirectionCosines"]], "reoblique (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.Reoblique"]], "reorientimageandmetadata (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.ReorientImageAndMetadata"]], "uniformgrid (class in sdcflows.interfaces.utils)": [[11, "sdcflows.interfaces.utils.UniformGrid"]], "sdcflows.interfaces.utils": [[11, "module-sdcflows.interfaces.utils"]], "b0fieldtransform (class in sdcflows.transform)": [[12, "sdcflows.transform.B0FieldTransform"]], "apply() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.apply"]], "coeffs (sdcflows.transform.b0fieldtransform attribute)": [[12, "sdcflows.transform.B0FieldTransform.coeffs"]], "disp_to_fmap() (in module sdcflows.transform)": [[12, "sdcflows.transform.disp_to_fmap"]], "fit() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.fit"]], "fmap_to_disp() (in module sdcflows.transform)": [[12, "sdcflows.transform.fmap_to_disp"]], "grid_bspline_weights() (in module sdcflows.transform)": [[12, "sdcflows.transform.grid_bspline_weights"]], "mapped (sdcflows.transform.b0fieldtransform attribute)": [[12, "sdcflows.transform.B0FieldTransform.mapped"]], "sdcflows.transform": [[12, "module-sdcflows.transform"]], "to_displacements() (sdcflows.transform.b0fieldtransform method)": [[12, "sdcflows.transform.B0FieldTransform.to_displacements"]], "unwarp_parallel() (in module sdcflows.transform)": [[12, "sdcflows.transform.unwarp_parallel"]], "worker() (in module sdcflows.transform)": [[12, "sdcflows.transform.worker"]], "sdcflows.utils": [[13, "module-sdcflows.utils"]], "estimatorregistry (class in sdcflows.utils.bimap)": [[14, "sdcflows.utils.bimap.EstimatorRegistry"]], "add() (sdcflows.utils.bimap.bidict method)": [[14, "sdcflows.utils.bimap.bidict.add"]], "bidict (class in sdcflows.utils.bimap)": [[14, "sdcflows.utils.bimap.bidict"]], "clear() (sdcflows.utils.bimap.bidict method)": [[14, "sdcflows.utils.bimap.bidict.clear"]], "get_key() (sdcflows.utils.bimap.estimatorregistry method)": [[14, "sdcflows.utils.bimap.EstimatorRegistry.get_key"]], "sdcflows.utils.bimap": [[14, "module-sdcflows.utils.bimap"]], "sources (sdcflows.utils.bimap.estimatorregistry property)": [[14, "sdcflows.utils.bimap.EstimatorRegistry.sources"]], "epi_mask() (in module sdcflows.utils.epimanip)": [[15, "sdcflows.utils.epimanip.epi_mask"]], "get_trt() (in module sdcflows.utils.epimanip)": [[15, "sdcflows.utils.epimanip.get_trt"]], "sdcflows.utils.epimanip": [[15, "module-sdcflows.utils.epimanip"]], "create_logger() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.create_logger"]], "front() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.front"]], "get_free_mem() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.get_free_mem"]], "last() (in module sdcflows.utils.misc)": [[16, "sdcflows.utils.misc.last"]], "sdcflows.utils.misc": [[16, "module-sdcflows.utils.misc"]], "au2rads() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.au2rads"]], "delta_te() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.delta_te"]], "phdiff2fmap() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.phdiff2fmap"]], "sdcflows.utils.phasemanip": [[17, "module-sdcflows.utils.phasemanip"]], "subtract_phases() (in module sdcflows.utils.phasemanip)": [[17, "sdcflows.utils.phasemanip.subtract_phases"]], "brain_masker() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.brain_masker"]], "deoblique_and_zooms() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.deoblique_and_zooms"]], "ensure_positive_cosines() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.ensure_positive_cosines"]], "reorient_pedir() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.reorient_pedir"]], "resample_to_zooms() (in module sdcflows.utils.tools)": [[18, "sdcflows.utils.tools.resample_to_zooms"]], "sdcflows.utils.tools": [[18, "module-sdcflows.utils.tools"]], "find_anatomical_estimators() (in module sdcflows.utils.wrangler)": [[19, "sdcflows.utils.wrangler.find_anatomical_estimators"]], "find_estimators() (in module sdcflows.utils.wrangler)": [[19, "sdcflows.utils.wrangler.find_estimators"]], "sdcflows.utils.wrangler": [[19, "module-sdcflows.utils.wrangler"]], "sdcflows.viz": [[20, "module-sdcflows.viz"]], "coolwarm_transparent() (in module sdcflows.viz.utils)": [[21, "sdcflows.viz.utils.coolwarm_transparent"]], "plot_registration() (in module sdcflows.viz.utils)": [[21, "sdcflows.viz.utils.plot_registration"]], "sdcflows.viz.utils": [[21, "module-sdcflows.viz.utils"]], "sdcflows.workflows": [[22, "module-sdcflows.workflows"]], "init_brainextraction_wf() (in module sdcflows.workflows.ancillary)": [[23, "sdcflows.workflows.ancillary.init_brainextraction_wf"]], "sdcflows.workflows.ancillary": [[23, "module-sdcflows.workflows.ancillary"]], "sdcflows.workflows.apply": [[24, "module-sdcflows.workflows.apply"]], "init_unwarp_wf() (in module sdcflows.workflows.apply.correction)": [[25, "sdcflows.workflows.apply.correction.init_unwarp_wf"]], "sdcflows.workflows.apply.correction": [[25, "module-sdcflows.workflows.apply.correction"]], "init_coeff2epi_wf() (in module sdcflows.workflows.apply.registration)": [[26, "sdcflows.workflows.apply.registration.init_coeff2epi_wf"]], "sdcflows.workflows.apply.registration": [[26, "module-sdcflows.workflows.apply.registration"]], "init_fmap_preproc_wf() (in module sdcflows.workflows.base)": [[27, "sdcflows.workflows.base.init_fmap_preproc_wf"]], "sdcflows.workflows.base": [[27, "module-sdcflows.workflows.base"]], "sdcflows.workflows.fit": [[28, "module-sdcflows.workflows.fit"]], "init_fmap_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_fmap_wf"]], "init_magnitude_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_magnitude_wf"]], "init_phdiff_wf() (in module sdcflows.workflows.fit.fieldmap)": [[29, "sdcflows.workflows.fit.fieldmap.init_phdiff_wf"]], "sdcflows.workflows.fit.fieldmap": [[29, "module-sdcflows.workflows.fit.fieldmap"]], "init_3dqwarp_wf() (in module sdcflows.workflows.fit.pepolar)": [[30, "sdcflows.workflows.fit.pepolar.init_3dQwarp_wf"]], "init_topup_wf() (in module sdcflows.workflows.fit.pepolar)": [[30, "sdcflows.workflows.fit.pepolar.init_topup_wf"]], "sdcflows.workflows.fit.pepolar": [[30, "module-sdcflows.workflows.fit.pepolar"]], "init_syn_preprocessing_wf() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.init_syn_preprocessing_wf"]], "init_syn_sdc_wf() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.init_syn_sdc_wf"]], "match_histogram() (in module sdcflows.workflows.fit.syn)": [[31, "sdcflows.workflows.fit.syn.match_histogram"]], "sdcflows.workflows.fit.syn": [[31, "module-sdcflows.workflows.fit.syn"]], "derivativesdatasink (class in sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.DerivativesDataSink"]], "init_fmap_derivatives_wf() (in module sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.init_fmap_derivatives_wf"]], "init_fmap_reports_wf() (in module sdcflows.workflows.outputs)": [[32, "sdcflows.workflows.outputs.init_fmap_reports_wf"]], "out_path_base (sdcflows.workflows.outputs.derivativesdatasink attribute)": [[32, "sdcflows.workflows.outputs.DerivativesDataSink.out_path_base"]], "sdcflows.workflows.outputs": [[32, "module-sdcflows.workflows.outputs"]]}}) \ No newline at end of file