ENH: Add fmap-jacobian to ignore list, thread through workflows

Author: effigies

fmriprep/cli/parser.py

@@ -285,7 +285,7 @@ def _slice_time_ref(value, parser):
         action="store",
         nargs="+",
         default=[],
-        choices=["fieldmaps", "slicetiming", "sbref", "t2w", "flair"],
+        choices=["fieldmaps", "slicetiming", "sbref", "t2w", "flair", "fmap-jacobian"],
         help="Ignore selected aspects of the input dataset to disable corresponding "
         "parts of the workflow (a space delimited list)",
     )

fmriprep/workflows/bold/apply.py

@@ -16,6 +16,7 @@ def init_bold_volumetric_resample_wf(
     *,
     metadata: dict,
     mem_gb: dict[str, float],
+    jacobian: bool,
     fieldmap_id: str | None = None,
     omp_nthreads: int = 1,
     name: str = 'bold_volumetric_resample_wf',
@@ -123,7 +124,7 @@ def init_bold_volumetric_resample_wf(
     boldref2target = pe.Node(niu.Merge(2), name='boldref2target', run_without_submitting=True)
     bold2target = pe.Node(niu.Merge(2), name='bold2target', run_without_submitting=True)
     resample = pe.Node(
-        ResampleSeries(),
+        ResampleSeries(jacobian=jacobian),
         name="resample",
         n_procs=omp_nthreads,
         mem_gb=mem_gb['resampled'],

fmriprep/workflows/bold/base.py

@@ -380,6 +380,7 @@ 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,
         name='bold_anat_wf',
     )
     bold_anat_wf.inputs.inputnode.resolution = "native"
@@ -437,6 +438,7 @@ 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,
             name='bold_std_wf',
         )
         ds_bold_std_wf = init_ds_volumes_wf(
@@ -521,6 +523,7 @@ 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,
             name='bold_MNI6_wf',
         )
 

fmriprep/workflows/bold/fit.py

@@ -838,7 +838,7 @@ def init_bold_native_wf(
 
     # Resample to boldref
     boldref_bold = pe.Node(
-        ResampleSeries(),
+        ResampleSeries(jacobian="fmap-jacobian" not in config.workflow.ignore),
         name="boldref_bold",
         n_procs=omp_nthreads,
         mem_gb=mem_gb["resampled"],