--2023-08-21 03:56:02-- https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz
-Resolving objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)... 134.70.24.1, 134.70.32.1, 134.70.28.1
+--2023-08-21 04:07:42-- https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz
+Resolving objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)... 134.70.24.1, 134.70.32.1, 134.70.28.1
Connecting to objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)|134.70.24.1|:443...
@@ -665,45 +663,48 @@ download test data ./sub-01_s 0%[ ] 119.17K 503KB/s
+ ./sub-01_s 0%[ ] 119.17K 498KB/s
+
+
+ ./sub-01_se 1%[ ] 920.00K 1.83MB/s
- ./sub-01_se 1%[ ] 920.00K 1.88MB/s
+ ./sub-01_ses 6%[> ] 4.40M 6.35MB/s
- ./sub-01_ses 5%[> ] 3.65M 5.37MB/s
+ ./sub-01_ses- 14%[=> ] 10.38M 11.2MB/s
- ./sub-01_ses- 14%[=> ] 10.35M 11.4MB/s
+ ./sub-01_ses-0 23%[===> ] 16.35M 14.4MB/s
- ./sub-01_ses-0 26%[====> ] 18.40M 16.6MB/s
+ ./sub-01_ses-01 32%[=====> ] 22.49M 16.9MB/s
- ./sub-01_ses-01 35%[======> ] 24.57M 18.8MB/s
+ ./sub-01_ses-01_ 41%[=======> ] 28.77M 18.7MB/s
- ./sub-01_ses-01_ 44%[=======> ] 30.57M 19.9MB/s
+ ./sub-01_ses-01_7 50%[=========> ] 35.05M 20.2MB/s
- ./sub-01_ses-01_7 53%[=========> ] 37.18M 21.5MB/s
+ ./sub-01_ses-01_7T 59%[==========> ] 41.07M 21.2MB/s
- ./sub-01_ses-01_7T 62%[===========> ] 43.26M 22.2MB/s
+./sub-01_ses-01_7T_ 68%[============> ] 47.44M 22.2MB/s
-./sub-01_ses-01_7T_ 72%[=============> ] 50.51M 23.5MB/s
+/sub-01_ses-01_7T_T 77%[==============> ] 53.70M 23.0MB/s
-/sub-01_ses-01_7T_T 82%[===============> ] 57.45M 24.4MB/s
+sub-01_ses-01_7T_T1 86%[================> ] 59.98M 23.7MB/s
-sub-01_ses-01_7T_T1 91%[=================> ] 63.48M 24.6MB/s
+ub-01_ses-01_7T_T1w 95%[==================> ] 65.99M 24.1MB/s
-./sub-01_ses-01_7T_ 100%[===================>] 69.32M 25.4MB/s in 2.7s
+./sub-01_ses-01_7T_ 100%[===================>] 69.32M 24.2MB/s in 2.9s
-2023-08-21 03:56:06 (25.4 MB/s) - ‘./sub-01_ses-01_7T_T1w_defaced.nii.gz’ saved [72682635/72682635]
+2023-08-21 04:07:45 (24.2 MB/s) - ‘./sub-01_ses-01_7T_T1w_defaced.nii.gz’ saved [72682635/72682635]
@@ -751,56 +752,56 @@ run nipype pipeline
-230821-03:56:10,270 nipype.interface WARNING:
+230821-04:07:49,905 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
-230821-03:56:23,140 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.140084:++ 3dedge3: AFNI version=AFNI_22.3.06 (Nov 15 2022) [64-bit]
+230821-04:08:02,709 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.709122:++ 3dedge3: AFNI version=AFNI_22.3.06 (Nov 15 2022) [64-bit]
-230821-03:56:23,142 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii to FLOAT32
+230821-04:08:02,711 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii to FLOAT32
-230821-03:56:23,143 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124: Warnings of this type will be muted for this session.
+230821-04:08:02,712 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496: Warnings of this type will be muted for this session.
-230821-03:56:23,143 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
+230821-04:08:02,713 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
-230821-03:56:23,145 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979:*+ WARNING: If you are performing spatial transformations on an oblique dset,
+230821-04:08:02,715 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093:*+ WARNING: If you are performing spatial transformations on an oblique dset,
-230821-03:56:23,146 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: such as /tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii,
+230821-04:08:02,715 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: such as /tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii,
-230821-03:56:23,146 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: or viewing/combining it with volumes of differing obliquity,
+230821-04:08:02,716 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: or viewing/combining it with volumes of differing obliquity,
-230821-03:56:23,147 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: you should consider running:
+230821-04:08:02,717 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: you should consider running:
-230821-03:56:23,148 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: 3dWarp -deoblique
+230821-04:08:02,718 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: 3dWarp -deoblique
-230821-03:56:23,149 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: on this and other oblique datasets in the same session.
+230821-04:08:02,719 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: on this and other oblique datasets in the same session.
-230821-03:56:23,150 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: See 3dWarp -help for details.
+230821-04:08:02,719 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: See 3dWarp -help for details.
-230821-03:56:23,150 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979:++ Oblique dataset:/tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii is 1.253358 degrees from plumb.
+230821-04:08:02,722 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093:++ Oblique dataset:/tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii is 1.253358 degrees from plumb.
@@ -896,7 +897,7 @@ run nipype pipeline
-
+
diff --git a/searchindex.js b/searchindex.js
index bb9371295..21b138f11 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
+Search.setIndex({"docnames": ["nipype_module_example"], "filenames": ["nipype_module_example.ipynb"], "titles": ["Basic Nipype Example"], "terms": {"author": 0, "steffen": 0, "bollmann": 0, "import": 0, "os": 0, "sy": 0, "in_colab": 0, "googl": 0, "colab": 0, "environ": 0, "ld_preload": 0, "apptainer_bindpath": 0, "content": 0, "tmp": 0, "cvmf": 0, "mplconfigdir": 0, "matplotlib": 0, "mpldir": 0, "lmod_cmd": 0, "usr": 0, "share": 0, "lmod": 0, "libexec": 0, "curl": 0, "j": 0, "o": 0, "http": 0, "raw": 0, "githubusercont": 0, "com": 0, "neurocommand": 0, "main": 0, "googlecolab_setup": 0, "sh": 0, "chmod": 0, "x": 0, "modulepath": 0, "join": 0, "map": 0, "str": 0, "list": 0, "lambda": 0, "path": 0, "abspath": 0, "ardc": 0, "edu": 0, "au": 0, "listdir": 0, "from": 0, "output": 0, "enable_custom_widget_manag": 0, "pip": 0, "instal": 0, "ipyniivu": 0, "cpu": 0, "inform": 0, "cat": 0, "proc": 0, "cpuinfo": 0, "grep": 0, "vendor": 0, "uniq": 0, "model": 0, "name": 0, "vendor_id": 0, 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\ No newline at end of file
diff --git a/structural_imaging/nipype_module_example.html b/structural_imaging/nipype_module_example.html
index 549e5626f..83f7750eb 100644
--- a/structural_imaging/nipype_module_example.html
+++ b/structural_imaging/nipype_module_example.html
@@ -67,7 +67,7 @@
const thebe_selector_output = ".output, .cell_output"
-
+
@@ -644,10 +644,8 @@ download test data
---2023-08-21 03:56:02-- https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz
-
-
-Resolving objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)... 134.70.24.1, 134.70.32.1, 134.70.28.1
+--2023-08-21 04:07:42-- https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz
+Resolving objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)... 134.70.24.1, 134.70.32.1, 134.70.28.1
Connecting to objectstorage.us-ashburn-1.oraclecloud.com (objectstorage.us-ashburn-1.oraclecloud.com)|134.70.24.1|:443...
@@ -665,45 +663,48 @@ download test data ./sub-01_s 0%[ ] 119.17K 503KB/s
+ ./sub-01_s 0%[ ] 119.17K 498KB/s
+
+
+ ./sub-01_se 1%[ ] 920.00K 1.83MB/s
- ./sub-01_se 1%[ ] 920.00K 1.88MB/s
+ ./sub-01_ses 6%[> ] 4.40M 6.35MB/s
- ./sub-01_ses 5%[> ] 3.65M 5.37MB/s
+ ./sub-01_ses- 14%[=> ] 10.38M 11.2MB/s
- ./sub-01_ses- 14%[=> ] 10.35M 11.4MB/s
+ ./sub-01_ses-0 23%[===> ] 16.35M 14.4MB/s
- ./sub-01_ses-0 26%[====> ] 18.40M 16.6MB/s
+ ./sub-01_ses-01 32%[=====> ] 22.49M 16.9MB/s
- ./sub-01_ses-01 35%[======> ] 24.57M 18.8MB/s
+ ./sub-01_ses-01_ 41%[=======> ] 28.77M 18.7MB/s
- ./sub-01_ses-01_ 44%[=======> ] 30.57M 19.9MB/s
+ ./sub-01_ses-01_7 50%[=========> ] 35.05M 20.2MB/s
- ./sub-01_ses-01_7 53%[=========> ] 37.18M 21.5MB/s
+ ./sub-01_ses-01_7T 59%[==========> ] 41.07M 21.2MB/s
- ./sub-01_ses-01_7T 62%[===========> ] 43.26M 22.2MB/s
+./sub-01_ses-01_7T_ 68%[============> ] 47.44M 22.2MB/s
-./sub-01_ses-01_7T_ 72%[=============> ] 50.51M 23.5MB/s
+/sub-01_ses-01_7T_T 77%[==============> ] 53.70M 23.0MB/s
-/sub-01_ses-01_7T_T 82%[===============> ] 57.45M 24.4MB/s
+sub-01_ses-01_7T_T1 86%[================> ] 59.98M 23.7MB/s
-sub-01_ses-01_7T_T1 91%[=================> ] 63.48M 24.6MB/s
+ub-01_ses-01_7T_T1w 95%[==================> ] 65.99M 24.1MB/s
-./sub-01_ses-01_7T_ 100%[===================>] 69.32M 25.4MB/s in 2.7s
+./sub-01_ses-01_7T_ 100%[===================>] 69.32M 24.2MB/s in 2.9s
-2023-08-21 03:56:06 (25.4 MB/s) - ‘./sub-01_ses-01_7T_T1w_defaced.nii.gz’ saved [72682635/72682635]
+2023-08-21 04:07:45 (24.2 MB/s) - ‘./sub-01_ses-01_7T_T1w_defaced.nii.gz’ saved [72682635/72682635]
@@ -751,56 +752,56 @@ run nipype pipeline
-230821-03:56:10,270 nipype.interface WARNING:
+230821-04:07:49,905 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
-230821-03:56:23,140 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.140084:++ 3dedge3: AFNI version=AFNI_22.3.06 (Nov 15 2022) [64-bit]
+230821-04:08:02,709 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.709122:++ 3dedge3: AFNI version=AFNI_22.3.06 (Nov 15 2022) [64-bit]
-230821-03:56:23,142 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii to FLOAT32
+230821-04:08:02,711 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii to FLOAT32
-230821-03:56:23,143 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124: Warnings of this type will be muted for this session.
+230821-04:08:02,712 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496: Warnings of this type will be muted for this session.
-230821-03:56:23,143 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.142124: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
+230821-04:08:02,713 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.711496: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
-230821-03:56:23,145 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979:*+ WARNING: If you are performing spatial transformations on an oblique dset,
+230821-04:08:02,715 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093:*+ WARNING: If you are performing spatial transformations on an oblique dset,
-230821-03:56:23,146 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: such as /tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii,
+230821-04:08:02,715 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: such as /tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii,
-230821-03:56:23,146 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: or viewing/combining it with volumes of differing obliquity,
+230821-04:08:02,716 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: or viewing/combining it with volumes of differing obliquity,
-230821-03:56:23,147 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: you should consider running:
+230821-04:08:02,717 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: you should consider running:
-230821-03:56:23,148 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: 3dWarp -deoblique
+230821-04:08:02,718 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: 3dWarp -deoblique
-230821-03:56:23,149 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: on this and other oblique datasets in the same session.
+230821-04:08:02,719 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: on this and other oblique datasets in the same session.
-230821-03:56:23,150 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979: See 3dWarp -help for details.
+230821-04:08:02,719 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093: See 3dWarp -help for details.
-230821-03:56:23,150 nipype.interface INFO:
- stderr 2023-08-21T03:56:23.144979:++ Oblique dataset:/tmp/tmp40icko7p/sub-01_ses-01_7T_T1w_defaced.nii is 1.253358 degrees from plumb.
+230821-04:08:02,722 nipype.interface INFO:
+ stderr 2023-08-21T04:08:02.715093:++ Oblique dataset:/tmp/tmpm70t_895/sub-01_ses-01_7T_T1w_defaced.nii is 1.253358 degrees from plumb.
@@ -896,7 +897,7 @@ run nipype pipeline
-
+