From 3fd1a3858ff147cc8d1c6171758e6f7a33439185 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sat, 18 Feb 2023 07:59:20 -0500 Subject: [PATCH 1/3] CI: Expect ribbon mask --- .circleci/ds005_bids_outputs.txt | 1 + .circleci/ds005_legacy_outputs.txt | 1 + .circleci/ds005_legacy_partial_outputs.txt | 1 + 3 files changed, 3 insertions(+) diff --git a/.circleci/ds005_bids_outputs.txt b/.circleci/ds005_bids_outputs.txt index f798c73f7..f1b51d8c5 100644 --- a/.circleci/ds005_bids_outputs.txt +++ b/.circleci/ds005_bids_outputs.txt @@ -16,6 +16,7 @@ bids/sub-01/anat/sub-01_desc-brain_mask.json bids/sub-01/anat/sub-01_desc-brain_mask.nii.gz bids/sub-01/anat/sub-01_desc-preproc_T1w.json bids/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz +bids/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz bids/sub-01/anat/sub-01_dseg.nii.gz bids/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt bids/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 diff --git a/.circleci/ds005_legacy_outputs.txt b/.circleci/ds005_legacy_outputs.txt index e8d037836..52d427f5e 100644 --- a/.circleci/ds005_legacy_outputs.txt +++ b/.circleci/ds005_legacy_outputs.txt @@ -16,6 +16,7 @@ fmriprep/sub-01/anat/sub-01_desc-brain_mask.json fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz +fmriprep/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz fmriprep/sub-01/anat/sub-01_dseg.nii.gz fmriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 diff --git a/.circleci/ds005_legacy_partial_outputs.txt b/.circleci/ds005_legacy_partial_outputs.txt index da7762830..8e5cdce69 100644 --- a/.circleci/ds005_legacy_partial_outputs.txt +++ b/.circleci/ds005_legacy_partial_outputs.txt @@ -16,6 +16,7 @@ fmriprep/sub-01/anat/sub-01_desc-brain_mask.json fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz +fmriprep/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz fmriprep/sub-01/anat/sub-01_dseg.nii.gz fmriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 From 9e0ba2fc0767caae322d9011ed94ff4ef2c0c5dc Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 17 Feb 2023 14:27:30 -0500 Subject: [PATCH 2/3] CI: Remove workflow directories with version information in --- .circleci/config.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 2ec0f97b6..7422f68c4 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -481,7 +481,7 @@ jobs: - run: name: Clean-up after anatomical run command: | - rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir* + rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir* rm -rf /tmp/${DATASET}/work/reportlets rm -rf /tmp/${DATASET}/derivatives/fmriprep - save_cache: @@ -529,10 +529,10 @@ jobs: mkdir -p /tmp/${DATASET}/derivatives_partial sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_partial sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_bids - sudo rm -rf /tmp/${DATASET}/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf + sudo rm -rf /tmp/${DATASET}/work_partial/fmriprep_*_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf # Nipype sometimes fails to pick up when the base directory changes # This is a cheap workflow, so let's not fuss - sudo rm -rf /tmp/${DATASET}/work /tmp/${DATASET}/work_bids/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf || true + sudo rm -rf /tmp/${DATASET}/work /tmp/${DATASET}/work_bids/fmriprep_*_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf || true - run: name: Checking outputs of full fMRIPrep run command: | @@ -688,7 +688,7 @@ jobs: - run: name: Clean-up after anatomical run command: | - rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir* + rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir* rm -rf /tmp/${DATASET}/work/reportlets rm -rf /tmp/${DATASET}/derivatives/fmriprep - save_cache: @@ -814,7 +814,7 @@ jobs: - run: name: Clean-up after anatomical run command: | - rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir* + rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir* rm -rf /tmp/${DATASET}/work/reportlets rm -rf /tmp/${DATASET}/derivatives/fmriprep - save_cache: From 6b9a3b7fcfa61105f0f19beeaff755141e14b18e Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 17 Feb 2023 14:34:19 -0500 Subject: [PATCH 3/3] CI: Fallback to non-fasttrack check, as this is not a failure --- .circleci/config.yml | 88 +++++------- .circleci/ds005_bids_fasttrack_outputs.txt | 66 ++++----- .circleci/ds005_bids_outputs.txt | 126 +++++++++--------- .circleci/ds005_legacy_fasttrack_outputs.txt | 2 +- .circleci/ds005_legacy_outputs.txt | 2 +- ...ds005_legacy_partial_fasttrack_outputs.txt | 2 +- .circleci/ds005_legacy_partial_outputs.txt | 2 +- .circleci/ds054_fasttrack_outputs.txt | 2 +- .circleci/ds054_outputs.txt | 2 +- .circleci/ds210_fasttrack_outputs.txt | 2 +- .circleci/ds210_outputs.txt | 2 +- 11 files changed, 139 insertions(+), 157 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 7422f68c4..d4683c0b8 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -87,6 +87,28 @@ _setup_fmriprep_docker: &setup_fmriprep_docker pip install --upgrade pip pip install --upgrade /tmp/src/fmriprep/wrapper/ +_check_outputs: &check_outputs + name: Checking outputs of fMRIPrep run + command: | + set +e -x + mkdir -p /tmp/${DATASET}/test + find /tmp/${DATASET}/${SUBDIR:-derivatives} \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) -prune -o -name "*" -print | cut -d/ -f 5- | sort > /tmp/${DATASET}/test/outputs.out + + FASTTRACK_OUTPUTS="${DATASET}${VARIANT}_fasttrack_outputs.txt" + FULL_OUTPUTS="${DATASET}${VARIANT}_outputs.txt" + RET=1 + if [ ! -f /tmp/.nofasttrack ]; then + echo "Checking fasttrack..." + diff /tmp/src/fmriprep/.circleci/${FASTTRACK_OUTPUTS} /tmp/${DATASET}/test/outputs.out + RET=$? + fi + if [ $RET -ne 0 ]; then + echo "Checking full..." + diff /tmp/src/fmriprep/.circleci/${FULL_OUTPUTS} /tmp/${DATASET}/test/outputs.out + RET=$? + fi + exit $RET + version: 2.1 aliases: @@ -534,16 +556,9 @@ jobs: # This is a cheap workflow, so let's not fuss sudo rm -rf /tmp/${DATASET}/work /tmp/${DATASET}/work_bids/fmriprep_*_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf || true - run: - name: Checking outputs of full fMRIPrep run - command: | - mkdir -p /tmp/${DATASET}/test - CHECK_OUTPUTS_FILE="${DATASET}_legacy_fasttrack_outputs.txt" - if [ -f /tmp/.nofasttrack ]; then - CHECK_OUTPUTS_FILE="${DATASET}_legacy_outputs.txt" - fi - find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out - diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out - exit $? + <<: *check_outputs + environment: + VARIANT: '_legacy' - run: name: Prepare BIDS Derivatives dataset command: | @@ -570,16 +585,10 @@ jobs: path: /tmp/ds005/bids destination: bids-run - run: - name: Checking outputs of partial fMRIPrep run - command: | - mkdir -p /tmp/${DATASET}/test - CHECK_OUTPUTS_FILE="${DATASET}_bids_fasttrack_outputs.txt" - if [ -f /tmp/.nofasttrack ]; then - CHECK_OUTPUTS_FILE="${DATASET}_bids_outputs.txt" - fi - find /tmp/${DATASET}/bids \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/++ | grep -v sourcedata | sort > /tmp/${DATASET}/test/outputs.out - diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out - exit $? + <<: *check_outputs + environment: + VARIANT: '_bids' + SUBDIR: 'bids' - run: name: Re-run fMRIPrep on single run of task data no_output_timeout: 2h @@ -605,17 +614,10 @@ jobs: path: /tmp/ds005/derivatives_partial destination: partial-run - run: - name: Checking outputs of partial fMRIPrep run - command: | - mkdir -p /tmp/${DATASET}/test - CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_fasttrack_outputs.txt" - if [ -f /tmp/.nofasttrack ]; then - CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_outputs.txt" - fi - sudo rm -rf /tmp/${DATASET}/derivatives_partial/freesurfer - find /tmp/${DATASET}/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives_partial/++ | sort > /tmp/${DATASET}/test/outputs.out - diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out - exit $? + <<: *check_outputs + environment: + VARIANT: '_legacy_partial' + SUBDIR: 'derivatives_partial' - run: name: Clean working directory when: on_success @@ -713,17 +715,7 @@ jobs: --fs-no-reconall --sloppy \ --output-spaces MNI152NLin2009cAsym:res-2 anat func \ --mem-mb 14336 --nthreads 4 -vv --debug compcor - - run: - name: Checking outputs of fMRIPrep - command: | - mkdir -p /tmp/${DATASET}/test - CHECK_OUTPUTS_FILE="${DATASET}_fasttrack_outputs.txt" - if [ -f /tmp/.nofasttrack ]; then - CHECK_OUTPUTS_FILE="${DATASET}_outputs.txt" - fi - find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out - diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out - exit $? + - run: *check_outputs - run: name: Generate report with one artificial error command: | @@ -853,17 +845,7 @@ jobs: --dummy-scans 1 --sloppy --write-graph \ --output-spaces MNI152NLin2009cAsym \ --mem-mb 14336 --nthreads 4 -vv - - run: - name: Checking outputs of fMRIPrep - command: | - mkdir -p /tmp/${DATASET}/test - CHECK_OUTPUTS_FILE="${DATASET}_fasttrack_outputs.txt" - if [ -f /tmp/.nofasttrack ]; then - CHECK_OUTPUTS_FILE="${DATASET}_outputs.txt" - fi - find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out - diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out - exit $? + - run: *check_outputs - run: name: Clean working directory when: on_success diff --git a/.circleci/ds005_bids_fasttrack_outputs.txt b/.circleci/ds005_bids_fasttrack_outputs.txt index 347697264..76e6721e0 100644 --- a/.circleci/ds005_bids_fasttrack_outputs.txt +++ b/.circleci/ds005_bids_fasttrack_outputs.txt @@ -1,33 +1,33 @@ -bids -bids/.bidsignore -bids/dataset_description.json -bids/desc-aparcaseg_dseg.tsv -bids/desc-aseg_dseg.tsv -bids/logs -bids/logs/CITATION.bib -bids/logs/CITATION.html -bids/logs/CITATION.md -bids/logs/CITATION.tex -bids/sub-01 -bids/sub-01/func -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json -bids/sub-01.html + +.bidsignore +dataset_description.json +desc-aparcaseg_dseg.tsv +desc-aseg_dseg.tsv +logs +logs/CITATION.bib +logs/CITATION.html +logs/CITATION.md +logs/CITATION.tex +sub-01 +sub-01/func +sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz +sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json +sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv +sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json +sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz +sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json +sub-01.html diff --git a/.circleci/ds005_bids_outputs.txt b/.circleci/ds005_bids_outputs.txt index f1b51d8c5..e7a635adf 100644 --- a/.circleci/ds005_bids_outputs.txt +++ b/.circleci/ds005_bids_outputs.txt @@ -1,63 +1,63 @@ -bids -bids/.bidsignore -bids/dataset_description.json -bids/desc-aparcaseg_dseg.tsv -bids/desc-aseg_dseg.tsv -bids/logs -bids/logs/CITATION.bib -bids/logs/CITATION.html -bids/logs/CITATION.md -bids/logs/CITATION.tex -bids/sub-01 -bids/sub-01/anat -bids/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz -bids/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz -bids/sub-01/anat/sub-01_desc-brain_mask.json -bids/sub-01/anat/sub-01_desc-brain_mask.nii.gz -bids/sub-01/anat/sub-01_desc-preproc_T1w.json -bids/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz -bids/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz -bids/sub-01/anat/sub-01_dseg.nii.gz -bids/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt -bids/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -bids/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt -bids/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -bids/sub-01/anat/sub-01_hemi-L_curv.shape.gii -bids/sub-01/anat/sub-01_hemi-L_inflated.surf.gii -bids/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii -bids/sub-01/anat/sub-01_hemi-L_pial.surf.gii -bids/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii -bids/sub-01/anat/sub-01_hemi-L_sulc.shape.gii -bids/sub-01/anat/sub-01_hemi-L_thickness.shape.gii -bids/sub-01/anat/sub-01_hemi-R_curv.shape.gii -bids/sub-01/anat/sub-01_hemi-R_inflated.surf.gii -bids/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii -bids/sub-01/anat/sub-01_hemi-R_pial.surf.gii -bids/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii -bids/sub-01/anat/sub-01_hemi-R_sulc.shape.gii -bids/sub-01/anat/sub-01_hemi-R_thickness.shape.gii -bids/sub-01/anat/sub-01_label-CSF_probseg.nii.gz -bids/sub-01/anat/sub-01_label-GM_probseg.nii.gz -bids/sub-01/anat/sub-01_label-WM_probseg.nii.gz -bids/sub-01/func -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii -bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json -bids/sub-01.html + +.bidsignore +dataset_description.json +desc-aparcaseg_dseg.tsv +desc-aseg_dseg.tsv +logs +logs/CITATION.bib +logs/CITATION.html +logs/CITATION.md +logs/CITATION.tex +sub-01 +sub-01/anat +sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz +sub-01/anat/sub-01_desc-aseg_dseg.nii.gz +sub-01/anat/sub-01_desc-brain_mask.json +sub-01/anat/sub-01_desc-brain_mask.nii.gz +sub-01/anat/sub-01_desc-preproc_T1w.json 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+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz +sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii +sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json +sub-01.html diff --git a/.circleci/ds005_legacy_fasttrack_outputs.txt b/.circleci/ds005_legacy_fasttrack_outputs.txt index 5c1f9d5d5..0eb29b842 100644 --- a/.circleci/ds005_legacy_fasttrack_outputs.txt +++ b/.circleci/ds005_legacy_fasttrack_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -39,4 +40,3 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.gii fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json fmriprep/sub-01.html -/tmp/ds005/derivatives diff --git a/.circleci/ds005_legacy_outputs.txt b/.circleci/ds005_legacy_outputs.txt index 52d427f5e..483805e82 100644 --- a/.circleci/ds005_legacy_outputs.txt +++ b/.circleci/ds005_legacy_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -69,4 +70,3 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.gii fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json fmriprep/sub-01.html -/tmp/ds005/derivatives diff --git a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt index f03d10c78..95fa6ee67 100644 --- a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt +++ b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -58,4 +59,3 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_ma fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz fmriprep/sub-01.html -/tmp/ds005/derivatives_partial diff --git a/.circleci/ds005_legacy_partial_outputs.txt b/.circleci/ds005_legacy_partial_outputs.txt index 8e5cdce69..e940c28a2 100644 --- a/.circleci/ds005_legacy_partial_outputs.txt +++ b/.circleci/ds005_legacy_partial_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -106,4 +107,3 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_ma fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz fmriprep/sub-01.html -/tmp/ds005/derivatives_partial diff --git a/.circleci/ds054_fasttrack_outputs.txt b/.circleci/ds054_fasttrack_outputs.txt index d04f229e8..ceaa84509 100644 --- a/.circleci/ds054_fasttrack_outputs.txt +++ b/.circleci/ds054_fasttrack_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -65,4 +66,3 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.nii.gz fmriprep/sub-100185.html -/tmp/ds054/derivatives diff --git a/.circleci/ds054_outputs.txt b/.circleci/ds054_outputs.txt index e9c54cc3e..bda5e0b1f 100644 --- a/.circleci/ds054_outputs.txt +++ b/.circleci/ds054_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -84,4 +85,3 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.nii.gz fmriprep/sub-100185.html -/tmp/ds054/derivatives diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt index ccd9e98ad..5e241caa8 100644 --- a/.circleci/ds210_fasttrack_outputs.txt +++ b/.circleci/ds210_fasttrack_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -38,4 +39,3 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-p fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_T2starmap.json fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_T2starmap.nii.gz fmriprep/sub-02.html -/tmp/ds210/derivatives diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt index 55e31c0c6..2d8b6036a 100644 --- a/.circleci/ds210_outputs.txt +++ b/.circleci/ds210_outputs.txt @@ -1,3 +1,4 @@ + fmriprep fmriprep/.bidsignore fmriprep/dataset_description.json @@ -57,4 +58,3 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-p fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_T2starmap.json fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_T2starmap.nii.gz fmriprep/sub-02.html -/tmp/ds210/derivatives