Merge pull request #392 from effigies/enh/report-t2w-flair-usage

ENH: Add T2w/FLAIR usage to boilerplate

Author: effigies

smriprep/workflows/anatomical.py

@@ -100,6 +100,7 @@ def init_anat_preproc_wf(
     spaces: SpatialReferences,
     precomputed: dict,
     omp_nthreads: int,
+    flair: list = (),  # Remove default after callers start passing it
     debug: bool = False,
     sloppy: bool = False,
     cifti_output: ty.Literal["91k", "170k", False] = False,
@@ -263,6 +264,7 @@ def init_anat_preproc_wf(
         spaces=spaces,
         t1w=t1w,
         t2w=t2w,
+        flair=flair,
         precomputed=precomputed,
         debug=debug,
         sloppy=sloppy,
@@ -446,6 +448,7 @@ def init_anat_fit_wf(
     spaces: SpatialReferences,
     precomputed: dict,
     omp_nthreads: int,
+    flair: list = (),  # Remove default after callers start passing it
     debug: bool = False,
     sloppy: bool = False,
     name="anat_fit_wf",
@@ -480,6 +483,7 @@ def init_anat_fit_wf(
                 msm_sulc=True,
                 t1w=['t1w.nii.gz'],
                 t2w=['t2w.nii.gz'],
+                flair=[],
                 skull_strip_mode='force',
                 skull_strip_template=Reference('OASIS30ANTs'),
                 spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
@@ -1033,6 +1037,11 @@ def init_anat_fit_wf(
         hires=hires,
         precomputed=precomputed,
     )
+    if t2w or flair:
+        t2w_or_flair = "T2-weighted" if t2w else "FLAIR"
+        surface_recon_wf.__desc__ += f"""\
+A {t2w_or_flair} image was used to improve pial surface refinement.
+"""
 
     # fmt:off
     workflow.connect([

smriprep/workflows/base.py

@@ -331,6 +331,7 @@ def init_single_subject_wf(
         subject_data = {
             "t1w": ["/completely/made/up/path/sub-01_T1w.nii.gz"],
             "t2w": [],
+            "flair": [],
         }
     else:
         subject_data = collect_data(layout, subject_id, bids_filters=bids_filters)[0]
@@ -427,6 +428,7 @@ def init_single_subject_wf(
         name="anat_preproc_wf",
         t1w=subject_data["t1w"],
         t2w=subject_data["t2w"],
+        flair=subject_data["flair"],
         omp_nthreads=omp_nthreads,
         output_dir=output_dir,
         skull_strip_fixed_seed=skull_strip_fixed_seed,