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FIX: restore cifti medial wall masking, subcortical volume LAS reorientation #298

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merged 2 commits into from
Jun 15, 2023
Merged

FIX: restore cifti medial wall masking, subcortical volume LAS reorientation #298

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739852e
restore cifti medial wall masking, subctx LAS orientation
madisoth Jun 15, 2023
0cb3621
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madisoth Jun 15, 2023
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19 changes: 14 additions & 5 deletions nibabies/workflows/bold/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1052,6 +1052,7 @@ def init_bold_grayords_wf(grayord_density, mem_gb, repetition_time, name="bold_g
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.utility import KeySelect

from ...interfaces.nibabel import ReorientImage
from ...interfaces.workbench import CiftiCreateDenseTimeseries

workflow = Workflow(name=name)
Expand Down Expand Up @@ -1137,9 +1138,16 @@ def init_bold_grayords_wf(grayord_density, mem_gb, repetition_time, name="bold_g
niu.Function(function=_split_surfaces, output_names=["left_surface", "right_surface"]),
name="split_surfaces",
)

reorient_data = pe.Node(ReorientImage(target_orientation="LAS"), name="reorient_data")
reorient_labels = reorient_data.clone(name="reorient_labels")

gen_cifti = pe.Node(CiftiCreateDenseTimeseries(timestep=repetition_time), name="gen_cifti")
gen_cifti.inputs.volume_structure_labels = str(
tf.api.get("MNI152NLin6Asym", resolution=2, atlas="HCP", suffix="dseg")
gen_cifti.inputs.roi_left = tf.api.get(
"fsLR", density=fslr_density, hemi="L", desc="nomedialwall", suffix="dparc"
)
gen_cifti.inputs.roi_right = tf.api.get(
"fsLR", density=fslr_density, hemi="R", desc="nomedialwall", suffix="dparc"
)
gen_cifti_metadata = pe.Node(
niu.Function(function=_gen_metadata, output_names=["out_metadata"]),
Expand All @@ -1149,9 +1157,10 @@ def init_bold_grayords_wf(grayord_density, mem_gb, repetition_time, name="bold_g

# fmt: off
workflow.connect([
(inputnode, gen_cifti, [
('subcortical_volume', 'volume_data'),
('subcortical_labels', 'volume_structure_labels')]),
(inputnode, reorient_data, [("subcortical_volume", "in_file")]),
(inputnode, reorient_labels, [("subcortical_labels", "in_file")]),
(reorient_data, gen_cifti, [("out_file", "volume_data")]),
(reorient_labels, gen_cifti, [("out_file", "volume_structure_labels")]),
(inputnode, select_fs_surf, [('surf_files', 'surf_files'),
('surf_refs', 'keys')]),
(select_fs_surf, resample, [('surf_files', 'in_file')]),
Expand Down