RF: Reuse cortical mask ROI and downsampled midthickness

Author: effigies

fmriprep/workflows/base.py

@@ -162,6 +162,7 @@ def init_single_subject_wf(subject_id: str):
         init_gifti_morphometrics_wf,
         init_hcp_morphometrics_wf,
         init_morph_grayords_wf,
+        init_resample_midthickness_wf,
     )
 
     from fmriprep.workflows.bold.base import init_bold_wf
@@ -435,6 +436,9 @@ def init_single_subject_wf(subject_id: str):
                 grayord_density=config.workflow.cifti_output,
                 omp_nthreads=omp_nthreads,
             )
+            resample_midthickness_wf = init_resample_midthickness_wf(
+                grayord_density=config.workflow.cifti_output,
+            )
             ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(
                 bids_root=bids_root,
                 output_dir=fmriprep_dir,
@@ -456,6 +460,13 @@ def init_single_subject_wf(subject_id: str):
                 (curv_wf, hcp_morphometrics_wf, [
                     ("outputnode.curv", "inputnode.curv"),
                 ]),
+                (anat_fit_wf, resample_midthickness_wf, [
+                    ('outputnode.midthickness', 'inputnode.midthickness'),
+                    (
+                        f"outputnode.sphere_reg_{'msm' if msm_sulc else 'fsLR'}",
+                        "inputnode.sphere_reg_fsLR",
+                    ),
+                ]),
                 (anat_fit_wf, morph_grayords_wf, [
                     ("outputnode.midthickness", "inputnode.midthickness"),
                     (
@@ -469,6 +480,9 @@ def init_single_subject_wf(subject_id: str):
                     ("outputnode.sulc", "inputnode.sulc"),
                     ("outputnode.roi", "inputnode.roi"),
                 ]),
+                (resample_midthickness_wf, morph_grayords_wf, [
+                    ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
+                ]),
                 (anat_fit_wf, ds_grayord_metrics_wf, [
                     ('outputnode.t1w_valid_list', 'inputnode.source_files'),
                 ]),
@@ -648,7 +662,6 @@ def init_single_subject_wf(subject_id: str):
                 ('outputnode.white', 'inputnode.white'),
                 ('outputnode.pial', 'inputnode.pial'),
                 ('outputnode.midthickness', 'inputnode.midthickness'),
-                ('outputnode.thickness', 'inputnode.thickness'),
                 ('outputnode.anat_ribbon', 'inputnode.anat_ribbon'),
                 (
                     f'outputnode.sphere_reg_{"msm" if msm_sulc else "fsLR"}',
@@ -696,6 +709,12 @@ def init_single_subject_wf(subject_id: str):
                 workflow.connect([
                     (select_MNI6_xfm, bold_wf, [("anat2std_xfm", "inputnode.anat2mni6_xfm")]),
                     (select_MNI6_tpl, bold_wf, [("brain_mask", "inputnode.mni6_mask")]),
+                    (hcp_morphometrics_wf, bold_wf, [
+                        ("outputnode.roi", "inputnode.cortex_mask"),
+                    ]),
+                    (resample_midthickness_wf, bold_wf, [
+                        ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
+                    ]),
                 ])  # fmt:skip
 
     return clean_datasinks(workflow)

fmriprep/workflows/bold/base.py

@@ -113,8 +113,6 @@ def init_bold_wf(
         FreeSurfer pial surfaces, in T1w space, collated left, then right
     sphere_reg_fsLR
         Registration spheres from fsnative to fsLR space, collated left, then right
-    thickness
-        FreeSurfer thickness metrics, collated left, then right
     anat_ribbon
         Binary cortical ribbon mask in T1w space
     fmap_id
@@ -235,7 +233,8 @@ def init_bold_wf(
                 "midthickness",
                 "pial",
                 "sphere_reg_fsLR",
-                "thickness",
+                "midthickness_fsLR",
+                "cortex_mask",
                 "anat_ribbon",
                 # Fieldmap registration
                 "fmap",
@@ -580,8 +579,9 @@ def init_bold_wf(
                 ("white", "inputnode.white"),
                 ("pial", "inputnode.pial"),
                 ("midthickness", "inputnode.midthickness"),
-                ("thickness", "inputnode.thickness"),
+                ("midthickness_fsLR", "inputnode.midthickness_fsLR"),
                 ("sphere_reg_fsLR", "inputnode.sphere_reg_fsLR"),
+                ("cortex_mask", "inputnode.cortex_mask"),
                 ("anat_ribbon", "inputnode.anat_ribbon"),
             ]),
             (bold_anat_wf, bold_fsLR_resampling_wf, [

fmriprep/workflows/bold/resampling.py

@@ -587,27 +587,28 @@ def init_bold_fsLR_resampling_wf(
         niu.IdentityInterface(
             fields=[
                 'bold_file',
+                'anat_ribbon',
                 'white',
                 'pial',
                 'midthickness',
-                'thickness',
+                'midthickness_fsLR',
                 'sphere_reg_fsLR',
-                'anat_ribbon',
+                'cortex_mask',
             ]
         ),
         name='inputnode',
     )
 
-    itersource = pe.Node(
+    hemisource = pe.Node(
         niu.IdentityInterface(fields=['hemi']),
-        name='itersource',
+        name='hemisource',
         iterables=[('hemi', ['L', 'R'])],
     )
 
     joinnode = pe.JoinNode(
         niu.IdentityInterface(fields=['bold_fsLR']),
         name='joinnode',
-        joinsource='itersource',
+        joinsource='hemisource',
     )
 
     outputnode = pe.Node(
@@ -622,9 +623,10 @@ def init_bold_fsLR_resampling_wf(
                 "white",
                 "pial",
                 "midthickness",
-                "thickness",
-                "sphere_reg",
+                'midthickness_fsLR',
+                "sphere_reg_fsLR",
                 "template_sphere",
+                'cortex_mask',
                 "template_roi",
             ],
             keys=["L", "R"],
@@ -648,20 +650,6 @@ def init_bold_fsLR_resampling_wf(
         str(atlases / 'R.atlasroi.32k_fs_LR.shape.gii'),
     ]
 
-    # Reimplements lines 282-290 of FreeSurfer2CaretConvertAndRegisterNonlinear.sh
-    initial_roi = pe.Node(CreateROI(), name="initial_roi", mem_gb=DEFAULT_MEMORY_MIN_GB)
-
-    # Lines 291-292
-    fill_holes = pe.Node(MetricFillHoles(), name="fill_holes", mem_gb=DEFAULT_MEMORY_MIN_GB)
-    native_roi = pe.Node(MetricRemoveIslands(), name="native_roi", mem_gb=DEFAULT_MEMORY_MIN_GB)
-
-    # Line 393 of FreeSurfer2CaretConvertAndRegisterNonlinear.sh
-    downsampled_midthickness = pe.Node(
-        SurfaceResample(method='BARYCENTRIC'),
-        name="downsampled_midthickness",
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
-
     # RibbonVolumeToSurfaceMapping.sh
     # Line 85 thru ...
     volume_to_surface = pe.Node(
@@ -689,23 +677,11 @@ def init_bold_fsLR_resampling_wf(
             ('white', 'white'),
             ('pial', 'pial'),
             ('midthickness', 'midthickness'),
-            ('thickness', 'thickness'),
-            ('sphere_reg_fsLR', 'sphere_reg'),
-        ]),
-        (itersource, select_surfaces, [('hemi', 'key')]),
-        # Native ROI file from thickness
-        (itersource, initial_roi, [('hemi', 'hemisphere')]),
-        (select_surfaces, initial_roi, [('thickness', 'thickness_file')]),
-        (select_surfaces, fill_holes, [('midthickness', 'surface_file')]),
-        (select_surfaces, native_roi, [('midthickness', 'surface_file')]),
-        (initial_roi, fill_holes, [('roi_file', 'metric_file')]),
-        (fill_holes, native_roi, [('out_file', 'metric_file')]),
-        # Downsample midthickness to fsLR density
-        (select_surfaces, downsampled_midthickness, [
-            ('midthickness', 'surface_in'),
-            ('sphere_reg', 'current_sphere'),
-            ('template_sphere', 'new_sphere'),
+            ('midthickness_fsLR', 'midthickness_fsLR'),
+            ('sphere_reg_fsLR', 'sphere_reg_fsLR'),
+            ('cortex_mask', 'cortex_mask'),
         ]),
+        (hemisource, select_surfaces, [('hemi', 'key')]),
         # Resample BOLD to native surface, dilate and mask
         (inputnode, volume_to_surface, [
             ('bold_file', 'volume_file'),
@@ -716,17 +692,17 @@ def init_bold_fsLR_resampling_wf(
             ('pial', 'outer_surface'),
         ]),
         (select_surfaces, metric_dilate, [('midthickness', 'surf_file')]),
+        (select_surfaces, mask_native, [('cortex_mask', 'mask')]),
         (volume_to_surface, metric_dilate, [('out_file', 'in_file')]),
-        (native_roi, mask_native, [('out_file', 'mask')]),
         (metric_dilate, mask_native, [('out_file', 'in_file')]),
         # Resample BOLD to fsLR and mask
         (select_surfaces, resample_to_fsLR, [
-            ('sphere_reg', 'current_sphere'),
+            ('sphere_reg_fsLR', 'current_sphere'),
             ('template_sphere', 'new_sphere'),
             ('midthickness', 'current_area'),
+            ('midthickness_fsLR', 'new_area'),
+            ('cortex_mask', 'roi_metric'),
         ]),
-        (downsampled_midthickness, resample_to_fsLR, [('surface_out', 'new_area')]),
-        (native_roi, resample_to_fsLR, [('out_file', 'roi_metric')]),
         (mask_native, resample_to_fsLR, [('out_file', 'in_file')]),
         (select_surfaces, mask_fsLR, [('template_roi', 'mask')]),
         (resample_to_fsLR, mask_fsLR, [('out_file', 'in_file')]),