feat(cli): Disable Jacobians by default except PEPOLAR, allow forcing

Author: effigies

fmriprep/cli/parser.py

@@ -347,7 +347,7 @@ def _slice_time_ref(value, parser):
         action='store',
         nargs='+',
         default=[],
-        choices=['bbr', 'no-bbr', 'syn-sdc'],
+        choices=['bbr', 'no-bbr', 'syn-sdc', 'fmap-jacobian'],
         help='Force selected processing choices, overriding automatic selections '
         '(a space delimited list).\n'
         ' * [no-]bbr: Use/disable boundary-based registration for BOLD-to-T1w coregistration\n'
@@ -801,12 +801,20 @@ def parse_args(args=None, namespace=None):
     config.from_dict(vars(opts), init=['nipype'])
 
     # Consistency checks
-    if 'bbr' in config.workflow.force and 'no-bbr' in config.workflow.force:
+    force_set = set(config.workflow.force)
+    ignore_set = set(config.workflow.ignore)
+    if {'bbr', 'no-bbr'} <= force_set:
         msg = (
             'Cannot force and disable boundary-based registration at the same time. '
             'Remove `bbr` or `no-bbr` from the `--force` options.'
         )
         raise ValueError(msg)
+    if 'fmap-jacobian' in force_set & ignore_set:
+        msg = (
+            'Cannot force and ignore fieldmap Jacobian correction. '
+            'Remove `fmap-jacobian` from either the `--force` or the `--ignore` option.'
+        )
+        raise ValueError(msg)
 
     if not config.execution.notrack:
         import importlib.util

fmriprep/workflows/base.py

@@ -566,6 +566,7 @@ def init_single_subject_wf(subject_id: str):
         for field in ['fmap', 'fmap_ref', 'fmap_coeff', 'fmap_mask', 'fmap_id', 'sdc_method']
     }
 
+    estimator_types = {est.bids_id: est.method for est in all_estimators}
     fmap_estimators = []
     if all_estimators:
         # Find precomputed fieldmaps that apply to this workflow
@@ -738,6 +739,15 @@ def init_single_subject_wf(subject_id: str):
     for bold_series in bold_runs:
         bold_file = bold_series[0]
         fieldmap_id = estimator_map.get(bold_file)
+        jacobian = False
+
+        if fieldmap_id:
+            if 'fmap-jacobian' in config.workflow.force:
+                jacobian = True
+            elif 'fmap-jacobian' not in config.workflow.ignore:
+                # Default behavior is to only use Jacobians for PEPOLAR fieldmaps
+                est_type = estimator_types[fieldmap_id]
+                jacobian = est_type == est_type.__class__.PEPOLAR
 
         functional_cache = {}
         if config.execution.derivatives:
@@ -758,6 +768,7 @@ def init_single_subject_wf(subject_id: str):
             bold_series=bold_series,
             precomputed=functional_cache,
             fieldmap_id=fieldmap_id,
+            jacobian=jacobian,
         )
         if bold_wf is None:
             continue

fmriprep/workflows/bold/base.py

@@ -57,6 +57,7 @@ def init_bold_wf(
     bold_series: list[str],
     precomputed: dict = None,
     fieldmap_id: str | None = None,
+    jacobian: bool = False,
 ) -> pe.Workflow:
     """
     This workflow controls the functional preprocessing stages of *fMRIPrep*.
@@ -253,6 +254,7 @@ def init_bold_wf(
         bold_series=bold_series,
         precomputed=precomputed,
         fieldmap_id=fieldmap_id,
+        jacobian=jacobian,
         omp_nthreads=omp_nthreads,
     )
 
@@ -292,6 +294,7 @@ def init_bold_wf(
     bold_native_wf = init_bold_native_wf(
         bold_series=bold_series,
         fieldmap_id=fieldmap_id,
+        jacobian=jacobian,
         omp_nthreads=omp_nthreads,
     )
 
@@ -383,7 +386,7 @@ def init_bold_wf(
         fieldmap_id=fieldmap_id if not multiecho else None,
         omp_nthreads=omp_nthreads,
         mem_gb=mem_gb,
-        jacobian='fmap-jacobian' not in config.workflow.ignore,
+        jacobian=jacobian,
         name='bold_anat_wf',
     )
     bold_anat_wf.inputs.inputnode.resolution = 'native'
@@ -443,7 +446,7 @@ def init_bold_wf(
             fieldmap_id=fieldmap_id if not multiecho else None,
             omp_nthreads=omp_nthreads,
             mem_gb=mem_gb,
-            jacobian='fmap-jacobian' not in config.workflow.ignore,
+            jacobian=jacobian,
             name='bold_std_wf',
         )
         ds_bold_std_wf = init_ds_volumes_wf(
@@ -550,7 +553,7 @@ def init_bold_wf(
             fieldmap_id=fieldmap_id if not multiecho else None,
             omp_nthreads=omp_nthreads,
             mem_gb=mem_gb,
-            jacobian='fmap-jacobian' not in config.workflow.ignore,
+            jacobian=jacobian,
             name='bold_MNI6_wf',
         )
 

fmriprep/workflows/bold/fit.py

@@ -97,6 +97,7 @@ def init_bold_fit_wf(
     bold_series: list[str],
     precomputed: dict = None,
     fieldmap_id: str | None = None,
+    jacobian: bool = False,
     omp_nthreads: int = 1,
     name: str = 'bold_fit_wf',
 ) -> pe.Workflow:
@@ -668,6 +669,7 @@ def init_bold_native_wf(
     *,
     bold_series: list[str],
     fieldmap_id: str | None = None,
+    jacobian: bool = False,
     omp_nthreads: int = 1,
     name: str = 'bold_native_wf',
 ) -> pe.Workflow:
@@ -875,7 +877,7 @@ def init_bold_native_wf(
 
     # Resample to boldref
     boldref_bold = pe.Node(
-        ResampleSeries(jacobian='fmap-jacobian' not in config.workflow.ignore),
+        ResampleSeries(jacobian=jacobian),
         name='boldref_bold',
         n_procs=omp_nthreads,
         mem_gb=mem_gb['resampled'],