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RF: Reuse cortical mask ROI and downsampled midthickness
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@effigies
effigies committed Nov 19, 2023
1 parent f0eff51 commit 691dd54
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Showing 3 changed files with 41 additions and 46 deletions.
21 changes: 20 additions & 1 deletion fmriprep/workflows/base.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand All @@ -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"),
(
Expand All @@ -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'),
]),
Expand Down Expand Up @@ -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"}',
Expand Down Expand Up @@ -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)
Expand Down
8 changes: 4 additions & 4 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -235,7 +233,8 @@ def init_bold_wf(
"midthickness",
"pial",
"sphere_reg_fsLR",
"thickness",
"midthickness_fsLR",
"cortex_mask",
"anat_ribbon",
# Fieldmap registration
"fmap",
Expand Down Expand Up @@ -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, [
Expand Down
58 changes: 17 additions & 41 deletions fmriprep/workflows/bold/resampling.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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"],
Expand All @@ -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(
Expand Down Expand Up @@ -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'),
Expand All @@ -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')]),
Expand Down

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