Merge pull request #316 from nipreps/enh/single-anat

ENH: Add separate workflow to run with a single anatomical

.circleci/bcp_anat_outputs.txt

@@ -51,5 +51,6 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
 sub-01_ses-1mo.html

.circleci/bcp_anat_t2only_outputs.txt

@@ -0,0 +1,54 @@
+.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/ses-1mo
+sub-01/ses-1mo/anat
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aparcaseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-ribbon_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T2w_mode-image_xfm.h5
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNIInfant+1_mode-image_xfm.h5
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-fsnative_mode-image_xfm.txt
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T2w_mode-image_xfm.txt
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01_ses-1mo.html

.circleci/bcp_full_outputs.txt

@@ -51,6 +51,7 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
 sub-01/ses-1mo/fmap
 sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-001_fmapid-auto00000_desc-coeff_fieldmap.nii.gz

.circleci/config.yml

@@ -397,6 +397,50 @@ jobs:
             pip install nibabel numpy nitransforms
             python /tmp/src/nibabies/scripts/check_outputs.py /tmp/${DATASET}/derivatives/nibabies
             exit $?
+      - run:
+          name: Create copy with only T2w data
+          command: |
+            mkdir -p /tmp/data/${DATASET}-t2only
+            cp /tmp/data/${DATASET}/dataset_description.json /tmp/data/${DATASET}-t2only
+            cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01
+            rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
+            tree /tmp/data/${DATASET}-t2only
+            mkdir -p /tmp/data/${DATASET}-t2only/derivatives
+            cp -r /tmp/data/${DATASET}/derivatives/precomputed /tmp/data/${DATASET}-t2only/derivatives
+            # rename the derivatives for now - this is only possible since they share the same space
+            sudo apt install rename
+            rename 's/space-T1w/space-T2w/' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*
+            sed -i 's/_T1w./_T2w./g' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*json
+            tree /tmp/data/${DATASET}-t2only/derivatives/precomputed
+
+      - run:
+          name: Run nibabies single anatomical workflow
+          no_output_timeout: 1h
+          command: |
+            mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only /tmp/${DATASET}/work-t2only
+            nibabies-wrapper docker /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only participant \
+                -i nipreps/nibabies:dev \
+                -e NIBABIES_DEV 1 --user $(id -u):$(id -g) \
+                --network none --notrack \
+                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work-t2only \
+                --fs-subjects-dir /tmp/data/${DATASET}/derivatives/infant-freesurfer \
+                --skull-strip-template UNCInfant:cohort-1 \
+                --output-spaces MNIInfant:cohort-1 func \
+                --sloppy --write-graph --mem-mb 14000 \
+                --nthreads 4 -vv --age-months 2 --sloppy \
+                --derivatives /tmp/data/${DATASET}-t2only/derivatives/precomputed \
+                --output-layout bids --anat-only
+      - run:
+          name: Checking outputs of T2-only nibabies anat
+          command: |
+            mkdir -p /tmp/${DATASET}/test
+            CHECK_OUTPUTS_FILE="${DATASET}_anat_t2only_outputs.txt"
+            cd /tmp/${DATASET}/derivatives/nibabies-t2only && tree -I 'figures|log' -lifa --noreport | sed s+^\./++ | sed '1d' | sort > /tmp/${DATASET}/test/outputs.out
+            cat /tmp/${DATASET}/test/outputs.out
+            sort -o /tmp/${DATASET}/test/expected.out /tmp/src/nibabies/.circleci/${CHECK_OUTPUTS_FILE}
+            diff /tmp/${DATASET}/test/expected.out /tmp/${DATASET}/test/outputs.out
+            rm -rf /tmp/${DATASET}/test
+            exit $?
       - store_artifacts:
           path: /tmp/bcp/derivatives
 

.pep8speaks.yml

@@ -0,0 +1,6 @@
+scanner:
+    diff_only: True
+    linter: pycodestyle
+
+pycodestyle:
+    max-line-length: 100

nibabies/utils/bids.py

@@ -281,7 +281,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             "MISSING_TSV_COLUMN_EEG_ELECTRODES",
             "MISSING_SESSION",
         ],
-        "error": ["NO_T1W"],
+        "error": [],
         "ignoredFiles": ["/dataset_description.json", "/participants.tsv"],
     }
     # Limit validation only to data from requested participants

nibabies/workflows/anatomical/__init__.py

@@ -1 +1 @@
-from .base import init_infant_anat_wf
+from .base import init_infant_anat_wf, init_infant_single_anat_wf