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Merge remote-tracking branch 'upstream/master' into enh/bids_filter
2 parents b12ffb8 + 4cb3385 commit 8976cc6

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‎.circleci/config.yml

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@@ -84,7 +84,7 @@ jobs:
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THISVERSION=${CIRCLE_TAG:-$THISVERSION}
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DOCKERVERSION=$(docker run --rm -it poldracklab/fmriprep:latest --version)
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DOCKERVERSION=${DOCKERVERSION%$'\r'}
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DOCKERVERSION=${DOCKERVERSION#*"fmriprep v"}
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DOCKERVERSION=${DOCKERVERSION#*"fMRIPrep v"}
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echo "VERSION: \"$THISVERSION\""
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echo "DOCKERVERSION: \"${DOCKERVERSION}\""
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test "$DOCKERVERSION" = "$THISVERSION"
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when: on_fail
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command: |
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sudo chown $(id -un):$(id -gn) -R /tmp/ds005
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find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
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find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
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-exec sh -c 'rm -f {}; touch {}' \;
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find /tmp/ds005/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
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find /tmp/ds005/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
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-exec sh -c 'rm -f {}; touch {}' \;
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- store_artifacts:
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--config $PWD/nipype.cfg -w /tmp/ds054/work \
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/tmp/data/ds054 /tmp/ds054/derivatives participant \
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--fs-no-reconall --sloppy --write-graph \
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--output-spaces MNI152NLin2009cAsym \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- run:
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name: Clean-up after anatomical run
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when: on_fail
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command: |
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sudo chown $(id -un):$(id -gn) -R /tmp/ds054
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find /tmp/ds054/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
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find /tmp/ds054/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
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-exec sh -c 'rm -f {}; touch {}' \;
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- store_artifacts:
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path: /tmp/ds054
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--config $PWD/nipype.cfg -w /tmp/ds210/work \
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/tmp/data/ds210 /tmp/ds210/derivatives participant \
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--fs-no-reconall --sloppy --write-graph \
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--output-spaces MNI152NLin2009cAsym \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- run:
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name: Clean-up after anatomical run
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--config $PWD/nipype.cfg -w /tmp/ds210/work \
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/tmp/data/ds210 /tmp/ds210/derivatives participant \
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--fs-no-reconall --t2s-coreg --use-syn-sdc \
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--template-resampling-grid native --dummy-scans 1 \
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--sloppy --write-graph --mem_mb 4096 --nthreads 2 -vv
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--dummy-scans 1 --sloppy --write-graph \
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--output-spaces MNI152NLin2009cAsym \
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--mem_mb 4096 --nthreads 2 -vv
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- run:
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name: Checking outputs of fMRIPrep
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command: |
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when: on_fail
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command: |
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sudo chown $(id -un):$(id -gn) -R /tmp/ds210
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find /tmp/ds210/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
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find /tmp/ds210/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
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-exec sh -c 'rm -f {}; touch {}' \;
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- store_artifacts:
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path: /tmp/ds210
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which fmriprep | grep sdist\\/bin
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INSTALLED_VERSION=$(fmriprep --version)
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INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
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INSTALLED_VERSION=${INSTALLED_VERSION#*"fmriprep v"}
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INSTALLED_VERSION=${INSTALLED_VERSION#*"fMRIPrep v"}
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echo "VERSION: \"$THISVERSION\""
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echo "INSTALLED: \"$INSTALLED_VERSION\""
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test "$INSTALLED_VERSION" = "$THISVERSION"
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which fmriprep | grep wheel\\/bin
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INSTALLED_VERSION=$(fmriprep --version)
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INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
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INSTALLED_VERSION=${INSTALLED_VERSION#*"fmriprep v"}
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INSTALLED_VERSION=${INSTALLED_VERSION#*"fMRIPrep v"}
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echo "VERSION: \"$THISVERSION\""
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echo "INSTALLED: \"$INSTALLED_VERSION\""
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test "$INSTALLED_VERSION" = "$THISVERSION"

‎.circleci/ds005_outputs.txt

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@@ -51,13 +51,13 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.tsv
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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-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsLR_den-91k_bold.dtseries.nii
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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
@@ -83,13 +83,13 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_ma
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
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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-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
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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

‎.circleci/ds005_partial_outputs.txt

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@@ -51,13 +51,13 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
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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-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
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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

‎.circleci/ds054_outputs.txt

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@@ -33,11 +33,11 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regre
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.nii.gz

‎.github/auto-comment.yml

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pullRequestOpened: |
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Thank your for raising your pull request.
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Some of the *fMRIPRep* maintainers will review your changes as soon as time permits.
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I'm attaching below a *Review Checklist* for the reviewers, to copy and paste
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it in their review comment.
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```markdown
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I'm attaching below a *Review Checklist* for the reviewers, to check off during the
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review.
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## PR Review
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*Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide*
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- [ ] As the reviewer I confirm that there are no conflicts of interest for me to review this work.
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Please check what applies in the following aspects of the PR:
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#### Code documentation
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2018
- [ ] New functions and modules are documented following the guidelines.
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- [ ] Existing code required amendments in documentation and has been updated.
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- [ ] Sufficient inline comments ensure readability by other contributors in the long term.
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#### Documentation site
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- [ ] The modifications to *fMRIPrep* in this PR **do not require extra documentation**. This is a common situation when a bug fix that does not change the code base substantially is submitted.
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- [ ] This PR requires documentation. The corresponding documentation will be submitted as an additional PR in the future.
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- [ ] This PR requires extra documentation, and will be included within this PR. Please check the boxes that apply best:
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- [ ] An existing feature is substantially modified, changing the interface and/or logic of a module.
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- [ ] A new feature is being added, therefore full documentation of it will be included
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- [ ] This PR addresses an error in existing documentation.
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- [ ] Yes, all expected sections of documentation were generated by the CI build, and look as expected
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#### Tests
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- [ ] The new functionalities in this PR are covered by the existing tests
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- [ ] New test batteries have been included with this PR
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#### Data
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- [ ] This PR does not require any additional data to be uploaded to OSF.
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- [ ] This PR requires additional data for tests.
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#### Dependencies: smriprep
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- [ ] This PR does not require any update on `smriprep`; or
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- [ ] `smriprep` has correctly been pinned.
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#### Dependencies: niworkflows
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- [ ] This PR does not require any update on `niworkflows`; or
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- [ ] `niworkflows` has correctly been pinned.
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#### Dependencies: sdcflows
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- [ ] This PR does not require any update on `sdcflows`; or
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- [ ] `sdcflows` has correctly been pinned.
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#### Dependencies: Nipype
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- [ ] This PR does not require any update on `nipype`; or
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- [ ] `nipype` has correctly been pinned.
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#### Dependencies: other
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- [ ] This PR does not require any update on other dependencies; or
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- [ ] other dependencies have correctly been pinned.
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#### Reports generated within CI tests
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- [ ] Yes, I have checked the reports of ds005 and they are not modified or the changes are as expected
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- [ ] Yes, I have checked the reports of ds054 and they are not modified or the changes are as expected
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- [ ] Yes, I have checked the reports of ds010 and they are not modified or the changes are as expected
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### Review Comments (other than those left inline with the code)
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```

‎.mailmap

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Adriana Rivera-Dompenciel <[email protected]>
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Adriana Rivera-Dompenciel <[email protected]> <[email protected]>
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Alejandro de la Vega <[email protected]>
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Alejandro de la Vega <[email protected]> delavega4
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Anibal Sólon Heinsfeld <[email protected]>
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Asier Erramuzpe <[email protected]>
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Christopher J. Markiewicz <[email protected]>
@@ -16,6 +18,8 @@ James D. Kent <[email protected]>
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James D. Kent <[email protected]> <[email protected]>
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James D. Kent <[email protected]> Fred Mertz <[email protected]>
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Jarod Roland <[email protected]>
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Karolina Finc <[email protected]>
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Karolina Finc <[email protected]> kfinc
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Kevin Sitek <[email protected]>
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Kevin Sitek <[email protected]> sitek <[email protected]>
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Krzysztof J. Gorgolewski <[email protected]>

‎.maint/contributors.json

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"name": "Cieslak, Matthew",
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"orcid": "0000-0002-1931-4734"
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},
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{
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"affiliation": "University of Texas at Austin",
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"name": "de la Vega, Alejandro",
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"orcid": "0000-0001-9062-3778"
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},
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{
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"affiliation": "Department of Psychiatry, McGill University",
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"name": "Finc, Karolina",
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"orcid": "0000-0002-0157-030X"
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},
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{
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"affiliation": "Department of Psychology, New York University, NY, USA",
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"name": "Groen, Iris I. A.",
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"orcid": "0000-0002-5536-6128"
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},
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{
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"affiliation": "Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen",
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"name": "Ye, Zhifang",
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"orcid": "0000-0003-0489-2619"
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}
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]
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]

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