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Merge branch 'master' of https://github.com/poldracklab/fmriprep 
2 parents ce35dd6 + 8fcc210 commit 6abb4da

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‎.circleci/config.yml

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@@ -21,7 +21,6 @@ jobs:
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- docker-v3-
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paths:
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- /tmp/cache/docker.tar.gz
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- /tmp/cache/ubuntu.tar.gz
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- checkout
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- setup_remote_docker
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- run:
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at: /tmp
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- restore_cache:
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keys:
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- ds005-anat-v12-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v12-{{ .Branch }}
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- ds005-anat-v12-master
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- ds005-anat-v12-
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- ds005-anat-v13-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v13-{{ .Branch }}
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- ds005-anat-v13-master
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- ds005-anat-v13-
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- run:
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name: Setting up test
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command: |
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--sloppy --write-graph --mem_mb 4096 \
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--nthreads 2 --anat-only -vv
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- save_cache:
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key: ds005-anat-v12-{{ .Branch }}-{{ epoch }}
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key: ds005-anat-v13-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds005/work
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- /tmp/ds005/derivatives/fmriprep
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- run:
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name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin)
@@ -415,7 +413,7 @@ jobs:
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--ignore-aroma-denoising-errors --use-aroma \
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--output-space T1w template fsaverage5 \
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--output-space T1w template fsaverage5 fsnative \
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--template-resampling-grid native \
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--use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
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--nthreads 2 --cifti-output -vv
@@ -442,7 +440,7 @@ jobs:
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--output-space T1w template fsaverage5 \
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--output-space T1w template fsaverage5 fsnative \
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--ignore-aroma-denoising-errors --use-aroma \
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--template-resampling-grid native \
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--nthreads 2 --cifti-output -vv
@@ -490,10 +488,10 @@ jobs:
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at: /tmp
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- restore_cache:
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keys:
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- ds054-anat-v10-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v10-{{ .Branch }}
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- ds054-anat-v10-master
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- ds054-anat-v10-
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- ds054-anat-v11-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v11-{{ .Branch }}
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- ds054-anat-v11-master
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- ds054-anat-v11-
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- run:
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name: Setting up test
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command: |
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--fs-no-reconall --sloppy --write-graph \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- save_cache:
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key: ds054-anat-v10-{{ .Branch }}-{{ epoch }}
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key: ds054-anat-v11-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds054/work
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- /tmp/ds054/derivatives
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- run:
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name: Run full fMRIPrep on ds054
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at: /tmp
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- restore_cache:
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keys:
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- ds210-anat-v8-{{ .Branch }}-{{ epoch }}
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- ds210-anat-v8-{{ .Branch }}
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- ds210-anat-v8-master
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- ds210-anat-v8-
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- ds210-anat-v9-{{ .Branch }}-{{ epoch }}
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- ds210-anat-v9-{{ .Branch }}
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- ds210-anat-v9-master
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- ds210-anat-v9-
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- run:
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name: Setting up test
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command: |
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--fs-no-reconall --sloppy --write-graph \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- save_cache:
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key: ds210-anat-v8-{{ .Branch }}-{{ epoch }}
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key: ds210-anat-v9-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds210/work
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- /tmp/ds210/derivatives
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- run:
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name: Run full fMRIPrep on ds000210

‎.circleci/ds005_outputs.txt

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@@ -41,6 +41,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regresso
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
@@ -59,6 +61,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regresso
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

‎.circleci/ds005_partial_outputs.txt

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@@ -41,6 +41,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regresso
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

‎CHANGES.rst

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@@ -1,3 +1,14 @@
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1.2.6-1 (January 24, 2019)
2+
==========================
3+
4+
Hotfix release of version 1.2.6, pinning niworkflows to a release version (instead
5+
of the development branch, since #1459) and including to bugfixes.
6+
7+
* [PIN] NiWorkflows 0.5.2.post7 (`1bf4a21 <https://github.com/poldracklab/fmriprep/commit/1bf4a21cce62c4330510a9a8ae50db876fbc23b0>`__).
8+
* [FIX] Bad ``fsnative`` replacement in CIfTI workflow (#1476) @oesteban
9+
* [FIX] Avoid warning when generating boilerplate (#1464) @oesteban
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11+
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1.2.6 (January 17, 2019)
213
========================
314

‎README.rst

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@@ -35,6 +35,9 @@ open-source software distribution.
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:target: https://doi.org/10.1038/s41592-018-0235-4
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:alt: Published in Nature Methods
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.. image:: https://img.shields.io/badge/RRID-SCR__016216-blue.svg
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:target: https://doi.org/10.1038/s41592-018-0235-4
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:alt: RRID:SCR_016216
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About
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-----

‎docs/environment.yml

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@@ -28,5 +28,5 @@ dependencies:
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- svgutils
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- nitime
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- nilearn
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- git+https://github.com/poldracklab/niworkflows.git@master#egg=niworkflows
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- niworkflows>=0.5.4,<0.6
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- tedana>=0.0.5

‎fmriprep/__about__.py

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'nilearn',
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'nipype>=1.1.6',
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'nitime',
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'niworkflows>=0.5.2.post5,<0.5.3',
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'niworkflows>=0.5.2.post7,<0.5.3',
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'numpy',
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'pandas',
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'psutil>=5.4',
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'pybids==0.6.5',
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'pyyaml',
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'scikit-image',
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'statsmodels',
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'tedana>=0.0.5',
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'psutil>=5.4',
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]
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104104

105105
LINKS_REQUIRES = [
106-
'git+https://github.com/poldracklab/niworkflows.git@'
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'master#egg=niworkflows',
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]
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TESTS_REQUIRES = [

‎fmriprep/cli/run.py

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'spaces (option "--output-space").'
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)
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584+
if opts.cifti_output and (opts.template != 'MNI152NLin2009cAsym' or
585+
'template' not in output_spaces):
586+
output_spaces.append('template')
587+
logger.warning(
588+
'Option "--cifti-output" requires functional images to be resampled to MNI space. '
589+
'The argument "template" has been automatically added to the list of output '
590+
'spaces (option "--output-space").'
591+
)
592+
584593
# Check output_space
585594
if 'template' not in output_spaces and (opts.use_syn_sdc or opts.force_syn):
586595
msg = ['SyN SDC correction requires T1 to MNI registration, but '
@@ -753,6 +762,7 @@ def build_workflow(opts, retval):
753762
cmd = ['pandoc', '-s', '--bibliography',
754763
pkgrf('fmriprep', 'data/boilerplate.bib'),
755764
'--filter', 'pandoc-citeproc',
765+
'--metadata', 'pagetitle="fMRIPrep citation boilerplate"',
756766
str(logs_path / 'CITATION.md'),
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'-o', str(logs_path / 'CITATION.html')]
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try:

‎fmriprep/workflows/bold/base.py

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@@ -779,10 +779,11 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
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781781
# SURFACES ##################################################################################
782-
if freesurfer and any(space.startswith('fs') for space in output_spaces):
782+
surface_spaces = [space for space in output_spaces if space.startswith('fs')]
783+
if freesurfer and surface_spaces:
783784
LOGGER.log(25, 'Creating BOLD surface-sampling workflow.')
784785
bold_surf_wf = init_bold_surf_wf(mem_gb=mem_gb['resampled'],
785-
output_spaces=output_spaces,
786+
output_spaces=surface_spaces,
786787
medial_surface_nan=medial_surface_nan,
787788
name='bold_surf_wf')
788789
workflow.connect([
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796797
])
797798

798799
# CIFTI output
799-
if cifti_output and 'template' in output_spaces:
800+
if cifti_output and surface_spaces:
800801
bold_surf_wf.__desc__ += """\
801802
*Grayordinates* files [@hcppipelines], which combine surface-sampled
802803
data and volume-sampled data, were also generated.
803804
"""
804805
gen_cifti = pe.MapNode(GenerateCifti(), iterfield=["surface_target", "gifti_files"],
805806
name="gen_cifti")
806807
gen_cifti.inputs.TR = metadata.get("RepetitionTime")
808+
gen_cifti.inputs.surface_target = [s for s in surface_spaces
809+
if s.startswith('fsaverage')]
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808811
workflow.connect([
809812
(bold_surf_wf, gen_cifti, [
810-
('targets.out', 'surface_target'),
811813
('outputnode.surfaces', 'gifti_files')]),
812814
(inputnode, gen_cifti, [('subjects_dir', 'subjects_dir')]),
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(bold_mni_trans_wf, gen_cifti, [('outputnode.bold_mni', 'bold_file')]),

‎fmriprep/workflows/bold/resampling.py

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@@ -84,6 +84,7 @@ def init_bold_surf_wf(mem_gb, output_spaces, medial_surface_nan, name='bold_surf
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BOLD series, resampled to FreeSurfer surfaces
8585
8686
"""
87+
# Ensure volumetric spaces do not sneak into this workflow
8788
spaces = [space for space in output_spaces if space.startswith('fs')]
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8990
workflow = Workflow(name=name)

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