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‎.circleci/artifact_path

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/0/tmp/src/fmriprep/docs/_build/html/index.html

‎.circleci/config.yml

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@@ -113,8 +113,9 @@ jobs:
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steps:
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- restore_cache:
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keys:
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- data-v6-{{ .Revision }}
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- data-v6-
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- data-v7-{{ .Branch }}-{{ .Revision }}
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- data-v7-{{ .Branch }}
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- data-v7-
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- run:
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name: Get test data from ds000005
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command: |
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- run:
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name: Get FreeSurfer derivatives for ds000005
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command: |
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if [[ ! -d /tmp/ds005/derivatives/freesurfer ]]; then
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mkdir -p /tmp/ds005/derivatives
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if [[ ! -d /tmp/ds005/freesurfer ]]; then
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mkdir -p /tmp/ds005
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wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180"
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tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005/derivatives
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tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005
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else
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echo "FreeSurfer derivatives of ds000005 were cached"
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fi
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- ds054/nipype.cfg
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- ds210/nipype.cfg
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- save_cache:
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key: data-v6-{{ .Revision }}-{{ epoch }}
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key: data-v7-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/data
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- /tmp/ds005/derivatives/freesurfer
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- /tmp/ds005/freesurfer
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test_pytest:
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machine:
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command: |
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apt-get update
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apt-get install -y graphviz
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- run:
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name: Install Requirements (may contain pinned versions)
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command: python -m pip install -r docs/requirements.txt
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- run:
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name: Install fMRIPrep
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command: python -m pip install ".[doc]"
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- docker-v3-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- data-v6-{{ .Revision }}
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- data-v7-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- ds005-anat-v15-{{ .Branch }}-{{ .Revision }}
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- ds005-anat-v15-{{ .Branch }}
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- ds005-anat-v15-master
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- ds005-anat-v15-
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- ds005-anat-v17-{{ .Branch }}-{{ .Revision }}
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- ds005-anat-v17-{{ .Branch }}
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- ds005-anat-v17-master
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- ds005-anat-v17-
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- run:
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name: Setting up test
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command: |
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--fs-subjects-dir /tmp/ds005/freesurfer \
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--skull-strip-template OASIS30ANTs:res-1 \
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--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
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--sloppy --write-graph --mem_mb 4096 \
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rm -rf /tmp/ds005/work/reportlets
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rm -rf /tmp/ds005/derivatives/fmriprep
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- save_cache:
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key: ds005-anat-v15-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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key: ds005-anat-v17-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/ds005/work
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--fs-subjects-dir /tmp/ds005/freesurfer \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--use-aroma \
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--skull-strip-template OASIS30ANTs:res-1 \
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name: Move intermediate results for second run
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command: |
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mkdir -p /tmp/ds005/derivatives_partial
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sudo mv /tmp/ds005/derivatives/freesurfer /tmp/ds005/derivatives_partial
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sudo cp -a /tmp/ds005/work /tmp/ds005/work_partial
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sudo rm -rf /tmp/ds005/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf
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- run:
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
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/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
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--fs-subjects-dir /tmp/ds005/freesurfer \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
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--aroma-melodic-dimensionality 2 --use-aroma \
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- docker-v3-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- data-v6-{{ .Revision }}
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- data-v7-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- ds054-anat-v13-{{ .Branch }}-{{ .Revision }}
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- ds054-anat-v13-{{ .Branch }}
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- ds054-anat-v13-master
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- ds054-anat-v13-
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- ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
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- ds054-anat-v14-{{ .Branch }}
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- ds054-anat-v14-master
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- ds054-anat-v14-
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- run:
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name: Setting up test
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command: |
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rm -rf /tmp/ds054/work/reportlets
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rm -rf /tmp/ds054/derivatives/fmriprep
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- save_cache:
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key: ds054-anat-v13-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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key: ds054-anat-v14-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/ds054/work
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- docker-v3-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- data-v6-{{ .Revision }}
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- data-v7-{{ .Branch }}-{{ .Revision }}
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- restore_cache:
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keys:
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- ds210-anat-v11-{{ .Branch }}-{{ .Revision }}
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- ds210-anat-v11-{{ .Branch }}-
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- ds210-anat-v11-master
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- ds210-anat-v11-
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- ds210-anat-v12-{{ .Branch }}-{{ .Revision }}
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- ds210-anat-v12-{{ .Branch }}-
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- ds210-anat-v12-master
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- ds210-anat-v12-
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- run:
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name: Setting up test
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command: |
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rm -rf /tmp/ds210/work/reportlets
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rm -rf /tmp/ds210/derivatives/fmriprep
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- save_cache:
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key: ds210-anat-v11-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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key: ds210-anat-v12-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/ds210/work
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‎.circleci/ds005_outputs.txt

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@@ -16,9 +16,9 @@ fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-orig_to-T1w_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5

‎.circleci/ds005_partial_outputs.txt

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@@ -16,9 +16,9 @@ fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-orig_to-T1w_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5

‎.circleci/ds054_outputs.txt

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fmriprep/sub-100185/anat/sub-100185_desc-preproc_T1w.nii.gz
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fmriprep/sub-100185/anat/sub-100185_dseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-100185/anat/sub-100185_from-orig_to-T1w_mode-image_xfm.txt
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fmriprep/sub-100185/anat/sub-100185_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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fmriprep/sub-100185/anat/sub-100185_label-CSF_probseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_label-GM_probseg.nii.gz

‎.circleci/ds210_outputs.txt

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fmriprep/sub-02/anat/sub-02_desc-preproc_T1w.nii.gz
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fmriprep/sub-02/anat/sub-02_dseg.nii.gz
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fmriprep/sub-02/anat/sub-02_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-02/anat/sub-02_from-orig_to-T1w_mode-image_xfm.txt
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fmriprep/sub-02/anat/sub-02_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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fmriprep/sub-02/anat/sub-02_label-CSF_probseg.nii.gz
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fmriprep/sub-02/anat/sub-02_label-GM_probseg.nii.gz

‎.github/config.yml

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# Comment to be posted to on PRs from first time contributors in your repository
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newPRWelcomeComment: >
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Thanks for opening this pull request!
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We have detected this is the first time for you to contribute
7-
to *fMRIPrep*.
8-
Please check out our [contributing guidelines](https://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md).
6+
It looks like this is your first time contributing to *fMRIPrep*. :smile:
97
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We invite you to list yourself as a *fMRIPrep* contributor, so if your name
11-
is not already mentioned, please modify the
12-
[``.zenodo.json``](https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json)
13-
file with your data right above Russ' entry. Example:
14-
15-
```
8+
We invite you to list yourself as an *fMRIPrep* contributor.
9+
To learn more about what that entails and how we credit our contributors,
10+
please check out the
11+
[contributing guidelines](https://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md#recognizing-contributions).
12+
If your name is not already on the list, please insert it, in alphabetical order, into the
13+
[``contributors.json`` file](https://github.com/poldracklab/fmriprep/blob/master/.maint/contributors.json).
14+
Example:
1615
16+
```JSON
1717
{
1818
"name": "Contributor, New FMRIPrep",
1919
"affiliation": "Department of fMRI prep'ing, Open Science Made-Up University",
2020
"orcid": "<your id>"
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},
22-
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{
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"name": "Poldrack, Russell A.",
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"affiliation": "Department of Psychology, Stanford University",
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"orcid": "0000-0001-6755-0259"
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},
28-
2922
```
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Of course, if you want to opt-out this time there is no
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problem at all with adding your name later.
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You will be always welcome to add it in the future whenever
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you feel it should be listed.
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you feel it should be listed.

‎.mailmap

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Adriana Rivera-Dompenciel <[email protected]>
2+
Adriana Rivera-Dompenciel <[email protected]> <[email protected]>
3+
Anibal Sólon Heinsfeld <[email protected]>
4+
Asier Erramuzpe <[email protected]>
5+
Christopher J. Markiewicz <[email protected]>
6+
Christopher J. Markiewicz <[email protected]> <[email protected]>
7+
Christopher J. Markiewicz <[email protected]> <[email protected]>
8+
Daniel J. Lurie <[email protected]>
9+
Elizabeth DuPre <[email protected]>
10+
Franklin Feingold <[email protected]>
11+
Franklin Feingold <[email protected]> <[email protected]>
12+
Franz Liem <[email protected]>
13+
Gabriel A. Devenyi <[email protected]>
14+
Ilkay Isik <[email protected]>
15+
James D. Kent <[email protected]>
16+
James D. Kent <[email protected]> <[email protected]>
17+
James D. Kent <[email protected]> Fred Mertz <[email protected]>
18+
Jarod Roland <[email protected]>
19+
Kevin Sitek <[email protected]>
20+
Kevin Sitek <[email protected]> sitek <[email protected]>
21+
Krzysztof J. Gorgolewski <[email protected]>
22+
Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
23+
Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-M6500.(none)>
24+
Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-M6500>
25+
Krzysztof J. Gorgolewski <[email protected]> <filo@filo-dtc-laptop>
26+
Krzysztof J. Gorgolewski <[email protected]> <filo@filolaptop>
27+
Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
28+
Marc Bue <[email protected]>
29+
Markus H. Sneve <[email protected]> <[email protected]>
30+
Mathias Goncalves <[email protected]>
31+
Mathias Goncalves <[email protected]> <[email protected]>
32+
Mathias Goncalves <[email protected]> <[email protected]>
33+
Matteo Visconti di Oleggio Castello <[email protected]>
34+
Mikael Naveau <[email protected]>
35+
Nir Jacoby <[email protected]>
36+
Nir Jacoby <[email protected]> <[email protected]>
37+
Oscar Esteban <[email protected]>
38+
Oscar Esteban <[email protected]> <[email protected]>
39+
Pablo Velasco <[email protected]>
40+
Rastko Ciric <[email protected]>
41+
Rastko Ciric <[email protected]> <[email protected]>
42+
Rastko Ciric <[email protected]> <[email protected]>
43+
Ross Blair <[email protected]>
44+
Ross Blair <[email protected]> <[email protected]>
45+
Romain Valabregue <[email protected]>
46+
Saren Seeley <[email protected]>
47+
Sebastian Urchs <[email protected]>
48+
Sebastien Naze <[email protected]>
49+
Shoshana Berleant <[email protected]> <[email protected]>
50+
William Hedley Thompson <[email protected]>
51+
William Hedley Thompson <[email protected]> <[email protected]>

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