Merge tag '20.2.0rc0' into halfpipe

20.2.0 RC0 (September 04, 2020)

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Revise the reproducibility of CompCor masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: FreeSurfer license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure NiPype telemetry is just pinged once (nipreps#2168)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin NiPype with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence PyBIDS warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)

.circleci/config.yml

@@ -297,43 +297,6 @@ jobs:
       - store_artifacts:
           path: /tmp/data/reports
 
-  build_docs:
-    docker:
-      - image: python:3.7.4
-    working_directory: /tmp/src/fmriprep
-    environment:
-      - FSLOUTPUTTYPE: 'NIFTI'
-    steps:
-      - checkout
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?docs\]' )" != "" ]]; then
-              echo "Skipping doc building job"
-              circleci step halt
-            fi
-      - run:
-          name: Check Python version and upgrade pip
-          command: |
-            python --version
-            python -m pip install -U pip
-      - run:
-          name: Install graphviz
-          command: |
-              apt-get update
-              apt-get install -y graphviz
-      - run:
-          name: Install Requirements (may contain pinned versions)
-          command: python -m pip install -r docs/requirements.txt
-      - run:
-          name: Install fMRIPrep
-          command: python -m pip install ".[doc]"
-      - run:
-          name: Build documentation
-          command: make SPHINXOPTS="-W" -C docs html
-      - store_artifacts:
-          path: /tmp/src/fmriprep/docs/_build/html
-
   ds005:
     machine:
       image: circleci/classic:201711-01
@@ -638,7 +601,7 @@ jobs:
                 ${FASTRACK_ARG} \
                 --fs-no-reconall --sloppy \
                 --output-spaces MNI152NLin2009cAsym:res-2 anat func \
-                --mem_mb 4096 --nthreads 2 -vv
+                --mem_mb 4096 --nthreads 2 -vv --debug compcor
       - run:
           name: Checking outputs of fMRIPrep
           command: |
@@ -653,10 +616,10 @@ jobs:
       - run:
           name: Generate report with one artificial error
           command: |
+            set -x
             sudo mv /tmp/${DATASET}/derivatives/fmriprep/sub-100185.html \
                     /tmp/${DATASET}/derivatives/fmriprep/sub-100185_noerror.html
-            UUID="$(date '+%Y%m%d-%H%M%S_')$(uuidgen)"
-            mkdir -p /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
+            UUID=$(grep uuid /tmp/${DATASET}/work/*/config.toml | cut -d\" -f 2)
             cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
                 /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
             set +e
@@ -666,7 +629,7 @@ jobs:
                 /tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
                 --fs-no-reconall --sloppy --write-graph \
                 --output-spaces MNI152NLin2009cAsym:res-2 anat func \
-                --reports-only --run-uuid $UUID
+                --reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
             RET=$?
             set -e
             [[ "$RET" -eq "1" ]]
@@ -1048,18 +1011,6 @@ workflows:
             tags:
               only: /.*/
 
-      - build_docs:
-          filters:
-            branches:
-              ignore:
-                - /tests?\/.*/
-                - /ds005\/.*/
-                - /ds054\/.*/
-                - /ds210\/.*/
-                - /docker\/.*/
-            tags:
-              only: /.*/
-
       - test_deploy_pypi:
           filters:
             branches:
@@ -1140,7 +1091,6 @@ workflows:
           requires:
             - test_deploy_pypi
             - test_pytest
-            - build_docs
             - ds005
             - ds054
             - ds210

.circleci/ds005_fasttrack_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -10,9 +11,11 @@ fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsaverage5_hemi-L_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsaverage5_hemi-R_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsLR_den-91k_bold.dtseries.json
@@ -42,9 +45,11 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-brain_mas
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-L_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-R_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsLR_den-91k_bold.dtseries.json

.circleci/ds005_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -51,9 +52,11 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsaverage5_hemi-L_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsaverage5_hemi-R_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-fsLR_den-91k_bold.dtseries.json
@@ -83,9 +86,11 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-brain_mas
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-L_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-R_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsLR_den-91k_bold.dtseries.json

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -10,9 +11,11 @@ fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-L_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsaverage5_hemi-R_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-fsLR_den-91k_bold.dtseries.json

.circleci/ds005_partial_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -51,9 +52,11 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.json

.circleci/ds054_fasttrack_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -10,10 +11,16 @@ fmriprep/sub-100185/func
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorA_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorC_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorT_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorW_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
@@ -27,10 +34,16 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-T1w_desc-prepro
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorA_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorC_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorT_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorW_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz

.circleci/ds054_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -29,10 +30,16 @@ fmriprep/sub-100185/func
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorA_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorC_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorT_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-CompCorW_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
@@ -46,10 +53,16 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-T1w_desc-prepro
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorA_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorC_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorT_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-CompCorW_mask.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz

.circleci/ds210_fasttrack_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -7,8 +8,10 @@ fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-02
 fmriprep/sub-02/func
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.json
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz

.circleci/ds210_outputs.txt

@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -26,8 +27,10 @@ fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
 fmriprep/sub-02/func
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.json
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-scanner_to-T1w_mode-image_xfm.txt
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz