Re-enable anat fasttrack for dataset without t1w (#3202)

Re-enables the possibility to run fMRIPrep on a fMRI only dataset using anat derivatives from another (anatomical) dataset with the same participant.

Tries to implement integration test for that feature.

fixes #3201 

related to #2201

Author: effigies

.circleci/config.yml

@@ -551,6 +551,21 @@ jobs:
           environment:
             VARIANT: '_partial'
             SUBDIR: 'fmriprep-partial'
+      - run:
+          name: Re-run fMRIPrep on single run of task data, without T1w in BIDS
+          no_output_timeout: 2h
+          command: |
+            rm -Rf /tmp/data/${DATASET}/sub-01/anat
+            FASTRACK_ARG="--derivatives anat=/tmp/${DATASET}/smriprep"
+            fmriprep-docker -i nipreps/fmriprep:latest \
+                -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
+                --network none \
+                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work_partial \
+                /tmp/data/${DATASET} /tmp/${DATASET}/fmriprep-partial-noT1w participant \
+                --fs-subjects-dir /tmp/${DATASET}/freesurfer \
+                ${FASTRACK_ARG} \
+                --sloppy --write-graph --mem-mb 14336 \
+                --level minimal --nthreads 4 -vv
       - run:
           name: Clean working directory
           when: on_success

fmriprep/cli/parser.py

@@ -825,7 +825,12 @@ def parse_args(args=None, namespace=None):
             "Making sure the input data is BIDS compliant (warnings can be ignored in most "
             "cases)."
         )
-        validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
+        validate_input_dir(
+            config.environment.exec_env,
+            opts.bids_dir,
+            opts.participant_label,
+            need_T1w=not config.execution.derivatives,
+        )
 
     # Setup directories
     config.execution.log_dir = config.execution.fmriprep_dir / "logs"

fmriprep/utils/bids.py

@@ -146,7 +146,7 @@ def write_derivative_description(bids_dir, deriv_dir):
     Path.write_text(deriv_dir / 'dataset_description.json', json.dumps(desc, indent=4))
 
 
-def validate_input_dir(exec_env, bids_dir, participant_label):
+def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
     # Ignore issues and warnings that should not influence FMRIPREP
     import subprocess
     import tempfile
@@ -196,7 +196,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             "MISSING_TSV_COLUMN_EEG_ELECTRODES",
             "MISSING_SESSION",
         ],
-        "error": ["NO_T1W"],
+        "error": ["NO_T1W"] if need_T1w else [],
         "ignoredFiles": ['/dataset_description.json', '/participants.tsv'],
     }
     # Limit validation only to data from requested participants

fmriprep/workflows/base.py

@@ -269,6 +269,7 @@ def init_single_subject_wf(subject_id: str):
             subject_data=subject_data,
             anat_only=config.workflow.anat_only,
             subject_id=subject_id,
+            anat_derivatives=anatomical_cache if anatomical_cache else None,
         ),
         name='bidssrc',
     )
@@ -338,9 +339,24 @@ def init_single_subject_wf(subject_id: str):
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
     )
 
+    # allow to run with anat-fast-track on fMRI-only dataset
+    if 't1w_preproc' in anatomical_cache and not subject_data['t1w']:
+        workflow.connect([
+            (bidssrc, bids_info, [(('bold', fix_multi_T1w_source_name), 'in_file')]),
+            (anat_fit_wf, summary, [('outputnode.t1w_preproc', 't1w')]),
+            (anat_fit_wf, ds_report_summary, [('outputnode.t1w_preproc', 'source_file')]),
+            (anat_fit_wf, ds_report_about, [('outputnode.t1w_preproc', 'source_file')]),
+        ])  # fmt:skip
+    else:
+        workflow.connect([
+            (bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
+            (bidssrc, summary, [('t1w', 't1w')]),
+            (bidssrc, ds_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
+            (bidssrc, ds_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
+        ])  # fmt:skip
+
     workflow.connect([
         (inputnode, anat_fit_wf, [('subjects_dir', 'inputnode.subjects_dir')]),
-        (bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
         (bidssrc, anat_fit_wf, [
             ('t1w', 'inputnode.t1w'),
             ('t2w', 'inputnode.t2w'),
@@ -350,10 +366,8 @@ def init_single_subject_wf(subject_id: str):
         (bids_info, anat_fit_wf, [(('subject', _prefix), 'inputnode.subject_id')]),
         # Reporting connections
         (inputnode, summary, [('subjects_dir', 'subjects_dir')]),
-        (bidssrc, summary, [('t1w', 't1w'), ('t2w', 't2w'), ('bold', 'bold')]),
+        (bidssrc, summary, [('t2w', 't2w'), ('bold', 'bold')]),
         (bids_info, summary, [('subject', 'subject_id')]),
-        (bidssrc, ds_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
-        (bidssrc, ds_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
         (summary, ds_report_summary, [('out_report', 'in_file')]),
         (about, ds_report_about, [('out_report', 'in_file')]),
     ])  # fmt:skip