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Merge pull request #316 from nipreps/enh/single-anat
ENH: Add separate workflow to run with a single anatomical
2 parents edcbd2b + bc7ee38 commit aa83bfa

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‎.circleci/bcp_anat_outputs.txt

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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
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sub-01_ses-1mo.html

‎.circleci/bcp_anat_t2only_outputs.txt

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.bidsignore
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dataset_description.json
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desc-aparcaseg_dseg.tsv
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desc-aseg_dseg.tsv
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logs
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logs/CITATION.bib
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logs/CITATION.html
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logs/CITATION.md
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logs/CITATION.tex
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sub-01
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sub-01/ses-1mo
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sub-01/ses-1mo/anat
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aparcaseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-ribbon_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T2w_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNIInfant+1_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-fsnative_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T2w_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-reg_sphere.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-reg_sphere.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
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sub-01_ses-1mo.html

‎.circleci/bcp_full_outputs.txt

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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
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sub-01/ses-1mo/fmap
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sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-001_fmapid-auto00000_desc-coeff_fieldmap.nii.gz

‎.circleci/config.yml

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pip install nibabel numpy nitransforms
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python /tmp/src/nibabies/scripts/check_outputs.py /tmp/${DATASET}/derivatives/nibabies
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exit $?
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- run:
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name: Create copy with only T2w data
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command: |
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mkdir -p /tmp/data/${DATASET}-t2only
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cp /tmp/data/${DATASET}/dataset_description.json /tmp/data/${DATASET}-t2only
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cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01
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rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
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tree /tmp/data/${DATASET}-t2only
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mkdir -p /tmp/data/${DATASET}-t2only/derivatives
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cp -r /tmp/data/${DATASET}/derivatives/precomputed /tmp/data/${DATASET}-t2only/derivatives
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# rename the derivatives for now - this is only possible since they share the same space
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sudo apt install rename
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rename 's/space-T1w/space-T2w/' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*
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sed -i 's/_T1w./_T2w./g' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*json
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tree /tmp/data/${DATASET}-t2only/derivatives/precomputed
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- run:
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name: Run nibabies single anatomical workflow
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no_output_timeout: 1h
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command: |
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mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only /tmp/${DATASET}/work-t2only
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nibabies-wrapper docker /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only participant \
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-i nipreps/nibabies:dev \
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-e NIBABIES_DEV 1 --user $(id -u):$(id -g) \
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--network none --notrack \
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--config $PWD/nipype.cfg -w /tmp/${DATASET}/work-t2only \
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--fs-subjects-dir /tmp/data/${DATASET}/derivatives/infant-freesurfer \
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--skull-strip-template UNCInfant:cohort-1 \
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--output-spaces MNIInfant:cohort-1 func \
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--sloppy --write-graph --mem-mb 14000 \
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--nthreads 4 -vv --age-months 2 --sloppy \
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--derivatives /tmp/data/${DATASET}-t2only/derivatives/precomputed \
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--output-layout bids --anat-only
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- run:
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name: Checking outputs of T2-only nibabies anat
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command: |
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mkdir -p /tmp/${DATASET}/test
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CHECK_OUTPUTS_FILE="${DATASET}_anat_t2only_outputs.txt"
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cd /tmp/${DATASET}/derivatives/nibabies-t2only && tree -I 'figures|log' -lifa --noreport | sed s+^\./++ | sed '1d' | sort > /tmp/${DATASET}/test/outputs.out
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cat /tmp/${DATASET}/test/outputs.out
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sort -o /tmp/${DATASET}/test/expected.out /tmp/src/nibabies/.circleci/${CHECK_OUTPUTS_FILE}
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diff /tmp/${DATASET}/test/expected.out /tmp/${DATASET}/test/outputs.out
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rm -rf /tmp/${DATASET}/test
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exit $?
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- store_artifacts:
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path: /tmp/bcp/derivatives
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‎.pep8speaks.yml

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scanner:
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diff_only: True
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linter: pycodestyle
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pycodestyle:
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max-line-length: 100

‎nibabies/utils/bids.py

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"MISSING_TSV_COLUMN_EEG_ELECTRODES",
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"MISSING_SESSION",
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],
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"error": ["NO_T1W"],
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"error": [],
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"ignoredFiles": ["/dataset_description.json", "/participants.tsv"],
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}
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# Limit validation only to data from requested participants

‎nibabies/workflows/anatomical/__init__.py

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from .base import init_infant_anat_wf
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from .base import init_infant_anat_wf, init_infant_single_anat_wf

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