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graddev integration#43

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akhanf wants to merge 231 commits intomasterkhanlab/hippunfold:masterfrom graddevkhanlab/hippunfold:graddevCopy head branch name to clipboard

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Commits on Jul 24, 2020

• Initial commit

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• initial commit

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• added pybids to dockerfile, and actually run the commands in run.py

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• build from v0.1 (minified container)

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Commits on Jul 30, 2020

• fix for combined affine reg

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• fixed handling of session in output folder

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• added template sphinx docs [skip ci]

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• added readthedocs config

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• added empty requirements.txt file

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• fix for rtd

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• changed theme for docs

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• added argparse sphinx ext, and created get_parser() in run.py to use it

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• updated requirements since rtd now needs to execute run.py

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• removed version [skip ci]

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• moved parser to separate file [skip ci]

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• added badges and link to readthedocs [skip ci]

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• added docker badge [skip ci]

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• added pipeline overview png to docs

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Commits on Aug 4, 2020

• updates for name change [skip ci]

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• updated help for argparse

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Commits on Sep 14, 2020

• rebuild from latest, after flirt reg fix

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Commits on Oct 9, 2020

• Hippocampal_AutoTop v0.2

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Commits on Oct 13, 2020

• added 1hr timeout to docker hub deployment

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Commits on Nov 13, 2020

• complete restructuring to snakebids app (#2)

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Commits on Nov 16, 2020

• relaxed dependencies for pip install

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• fix typo in setup.py

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Commits on Nov 20, 2020

• Manual segmentation as input (#9)

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Commits on Nov 23, 2020

• deep model training skeleton in place; will need to discuss dependencies

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• compatibility with matlab run_niftynet [skip ci]

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• typo [skip ci]

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Commits on Nov 25, 2020

• pulled latest autotop with gifti, updated dockerfile (untested)

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• updated instructions in readme

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• updated to realpath for container

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• set all rules to use same execution group (subj) for scaling up to many subjects

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Commits on Nov 26, 2020

• initial stab at incorporating gifti

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• updated to lastest autotop

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Commits on Dec 3, 2020

• fixed cnn names, container path

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• set autotopdir, change in autotop params order

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Commits on Dec 4, 2020

• updated to latest autotop

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Commits on Dec 9, 2020

• removed template as a wildcard

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• added full grid unfolded space correction

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• added more surface processing and spec file creation

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• some fixes to get spec files generated

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• added --skip_preproc and --skip_coreg, implemented them for T2w (still need to do T1w, dwi)

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Commits on Dec 10, 2020

• implemented skip_preproc for T1w

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• added cropT1w ref space for outputs, generated old subfield seg and coords

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• condensed to single all rule

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• fix for propagating coords

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• fixed cropT1w padding, and added subfield from surface creation

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• Merge pull request #13 from khanlab/dev

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• change to a PR branch on autotop for now

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• Merge pull request #14 from khanlab/dev

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• more support for retraining/fineTuning UNet. Testing still required.

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• Merge branch 'master' of https://github.com/khanlab/hippunfold

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Commits on Dec 11, 2020

• moved autotop back to master branch, after PR#21

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Commits on Dec 12, 2020

• added scipy dep

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• fixed time bug, MultiLabel interp, added subfieldswithtissue

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• python script for labelling subfields from vol coords

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Commits on Dec 13, 2020

• reorg to make proper package

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• removed submodule (to move it)

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• added submodule in subfolder

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• moved workflow and resources to module dir

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• changed container to autotop wherever possible

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• more updates

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• fix input args for autotop

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Commits on Dec 14, 2020

• Merge pull request #15 from khanlab/dev

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• updates to autotop for mcr

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• removed setting AUTOTOP_DIR, is set in rule

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• Merge branch 'master' into packaging

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• fix for itk threads, autotop mansegs

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• updated comment to deprecate non-mcr version

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• updates to readme

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• Merge pull request #16 from khanlab/packaging

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• Update README.md

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• Update README.md

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• update to test re-enabled circleci

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• major refactoring of docs, some packaging updates

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• update to only build on master branch [skip ci]

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• Merge pull request #17 from khanlab/docs

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Commits on Dec 15, 2020

• fix requirements for docs [skip ci]

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• updated path to png in readme [skip ci]

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Commits on Dec 16, 2020

• bugfix for moved ref nii file, added constrain surf py, fix for T1w (no invert)

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Commits on Jan 5, 2021

• updated overview fig link so it appears in docs [skip ci]

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Commits on Jan 12, 2021

• changed to recursive checkout (to get submodule)

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• changed checkout to use http (hardcoded for now)

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• changed to clone into curr dir

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Commits on Jan 15, 2021

• added CNNmodel: 1mmT1w (#23)

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Commits on Jan 17, 2021

• updates for nnunet instead of niftynet for T2w

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• refactoring for subfield processing, moved rules out of autotop.smk, removed unused/deprecated rules

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• modifying nnunet to use shadow (untested)

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• forgot to cp input image in nnunet

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• updates to naming

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Commits on Jan 18, 2021

• changed autotop time to 3hrs to force longer walltime for grouped job

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• added hippunfold_download_models helper script

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Commits on Jan 19, 2021

• added cmdline option for rigid reg to template

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• some incidental clean-up in config

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Commits on Jan 26, 2021

• added test datasets

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• refactoring to organize results/ and work/ and remove unnecessary files

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Commits on Jan 27, 2021

• added and uploaded new T1w nnunet model

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• removed 1mmT1w (no longer needed for nnunet because of blurring augmentation)

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• fix in all rule for cropT1w anat

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• updated regex for nnunet Task to work with new model name as well

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Commits on Jan 28, 2021

• added env var for model cache, and pre-downloading in Dockerfile

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• Merge pull request #27 from khanlab/modelsincontainer

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• use stream=True in get() to avoid circleci mem error

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• renamed and reorganized surf gifti files

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• cleaned up config file, replaced hardcoded containers

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Commits on Jan 29, 2021

• Merge pull request #28 from khanlab/docs

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Commits on Jan 31, 2021

• changed to yingli branch to test cpu-only inference

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• added visqc scripts from snakedwi

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• added vis for subfields, template reg, subfield vols

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Commits on Feb 1, 2021

• added use_gpu rule (disabled by default to save resources)

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• hotfix for custom downloaded model path in nnunet

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• added option to disable test-time augmentation

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• Merge pull request #31 from khanlab/cpu_inference

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Commits on Feb 4, 2021

• added group analysis_level for compiling tsv

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Commits on Feb 8, 2021

• hippb500, output_spaces

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Commits on Feb 23, 2021

• Merge pull request #32 from khanlab/visqc

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Commits on Feb 25, 2021

• minor clarifications (#29)

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Commits on Feb 26, 2021

• bugfix qc rule

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Commits on Feb 27, 2021

• add composed itk warps from T1w to unfold (incl corobl to unfold) (#36)

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Commits on Mar 2, 2021

• Add dependencies for report generation (#37)

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• add graphviz-dev dependency to Dockerfile

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• change to libgraphviz-dev in Dockerfile

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• upgraded to autotop_deps v0.3 container

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• Merge branch 'master' into hippdwi

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• added unfold to list of default output_spaces

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• added b500 test case

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Commits on Mar 3, 2021

• updated test cases

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• fixes to get tests passing

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Commits on Mar 7, 2021

• Manualseg (#34)

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Commits on Mar 22, 2021

• added missing final transform as target rule

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• Merge pull request #44 from khanlab/xfm-patch

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Commits on Mar 30, 2021

• added longitudinal test data

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Commits on Mar 31, 2021

• Merge pull request #47 from khanlab/longitudinal_tests [skip ci]

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• Merge branch 'master' into hippdwi

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• set ref space for transforms

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Commits on Apr 1, 2021

• upgrade to v0.3.0

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• updated boilerplate for snakebids v0.3.0

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• fix typo

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• yet another typo

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Commits on Apr 15, 2021

• update to latest (v0.3.6)

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Commits on Apr 20, 2021

• added missing testcase for modality=segT2w

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• fixes segT2w bug, missing outputs in a rule

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• fix for segT2w, sets bg overlay image properly

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• pin snakebids version to 0.2.1

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• Merge pull request #51 from khanlab/patch-segT2w

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• Merge branch 'master' into snakebids-v0.3.0

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• Merge branch 'master' into hippdwi

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• Merge pull request #49 from khanlab/snakebids-v0.3.0

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• Merge pull request #38 from khanlab/hippdwi

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Commits on Apr 21, 2021

• some additions to CIFTI outputs (#41)

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Commits on Apr 23, 2021

• upgrade to snakebids 0.3.9 to fix --help_snakemake

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Commits on Apr 24, 2021

• bump version

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• Merge pull request #52 from khanlab/v0.4.0rc

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Commits on Apr 26, 2021

• added additional pngs for QC but cant find where to specify these new outputs in Snakefile

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• found it, testing now

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Commits on Apr 27, 2021

• naming updated; tested successfully

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Commits on Apr 28, 2021

• upgrade Dockerfile to autotop_deps:v0.3.1

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Commits on Apr 29, 2021

• Merge pull request #58 from khanlab/akhanf-patch-1

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Commits on May 3, 2021

• split into dseg and surf

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Commits on May 13, 2021

• fix in create_spec_file

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• Merge pull request #61 from khanlab/akhanf-patch-1

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• Update setup.py

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• Merge pull request #62 from khanlab/akhanf-patch-1

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Commits on May 15, 2021

• Merge pull request #57 from khanlab/moreQCimgs

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• change snakebids version in docs to get --path_*

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Commits on May 16, 2021

• Merge pull request #55 from khanlab/docs-update

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Commits on May 17, 2021

• Refactor targets (#63)

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Commits on May 19, 2021

• integrate into snakemake workflow, various fixes

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• Merge branch 'master' into nomatlab

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• fix for inputseg, removed extraneous rules

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Commits on May 20, 2021

• bugfixes to get laplace running

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• WIP create warps

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• fixed accidental line deletion

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Commits on May 21, 2021

• Update Dockerfile

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• some more progress, still WIP

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• should be functional now, with warp extrapolation missing

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• resources all in one place. can soon remove hippunfold/hippocampal_autotop entirely!

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Commits on May 22, 2021

• shape inject, laplace, and more refactoring

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• fix typo in config

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• updated container

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• updated to use autotop container wherever possible

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• removed hippocampal_autotop submodule

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• bugfixes to get running, disabled midsurf vis

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Commits on May 24, 2021

• laplace with init, new heuristic for PD sink

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Commits on May 25, 2021

• revert to not use new PD sink

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• revert new pd sink in config files

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• fix when reverting to old template coords

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• added fix for missing shapeinject labels (require re-install)

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Commits on May 27, 2021

• fix bug in inputfunction for template_shape_reg

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• add astropy dependency

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• reduced memory usage estimate

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• actual for for template_shape_ref input function

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• archive work by default, moved qc to results

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• updated max iters and added time to laplace

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• added --skip_inject_template_labels option (#71)

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Commits on May 28, 2021

• bugfix: was requiring t2 to t1 warp for resampling to cropT1w space with --skip_coreg (#70)

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• Delete template_shape_inject.sh

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• Update MANIFEST.in

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• Merge pull request #64 from khanlab/nomatlab

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• additions for pypi, bumpversion

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• changed nnunet to new pypi dependency

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• Merge pull request #72 from khanlab/pypi #minor

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• fix bumpversion to master branch #minor

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• edit to trigger bump #minor

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• another attempted fix for bumpversion #minor

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• back to PAT, all perms #minor [skip ci]

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• commit to trigger bumpversion again #minor

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• Bump version: 0.4.0 → 0.5.0

  

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Commits on Jun 1, 2021

• pin numpy version

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• bugfixes in itk warps

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• minor fix, had wrong warp as dependency in map_to_full_grid

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• Merge pull request #73 from khanlab/patch-swap-itkwarps

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• Bump version: 0.5.0 → 0.5.1

  

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• initial import of new files

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• added python script and rule for jacobian

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• bugfix warp orientation, added composed warps

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• added compose_warps.smk to the workflow

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• added unfold2native composite warps to targets

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• bugfix in target rules

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• Added nan masks for gradient

  

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• Added generic python rule and script to compute the graddev from the jacobian

  

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• bids compliance

  

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• Updated graddev and jacobian scripts to deal with boundary issues

  

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• Update compute_graddev.py

  

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• Added test case to debug transformation to unfolded space

  

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• some updates to get test workflow runnable

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• updates compose_warps with nomatlab changes

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Commits on Jun 2, 2021

• Update compute_jacobian.py

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• Added test file

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