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FEAT: Save CIFTI subcortical volumes #357

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FEAT: Save CIFTI subcortical volumes #357

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4 changes: 4 additions & 0 deletions nibabies/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,6 +366,7 @@ def init_func_preproc_wf(bold_file, spaces, has_fieldmap=False, existing_derivat
"bold_mask_native",
"bold_echos_native",
"bold_cifti",
"bold_rois",
"bold2anat_xfm",
"cifti_metadata",
"surfaces",
Expand Down Expand Up @@ -456,6 +457,7 @@ def init_func_preproc_wf(bold_file, spaces, has_fieldmap=False, existing_derivat
('nonaggr_denoised_file', 'inputnode.nonaggr_denoised_file'),
('bold_cifti', 'inputnode.bold_cifti'),
('cifti_metadata', 'inputnode.cifti_metadata'),
('bold_rois', 'inputnode.bold_rois'),
('t2star_bold', 'inputnode.t2star_bold'),
('t2star_t1', 'inputnode.t2star_t1'),
('t2star_std', 'inputnode.t2star_std'),
Expand Down Expand Up @@ -991,6 +993,8 @@ def init_func_preproc_wf(bold_file, spaces, has_fieldmap=False, existing_derivat
(subcortical_rois_wf, subcortical_mni_alignment_wf, [
("outputnode.MNIInfant_rois", "inputnode.MNIInfant_rois"),
("outputnode.MNI152_rois", "inputnode.MNI152_rois")]),
(subcortical_mni_alignment_wf, outputnode, [
("outputnode.subcortical_volume", "bold_rois")]),

# CIFTI surface sampling
(inputnode, bold_fsLR_resampling_wf, [
Expand Down
22 changes: 21 additions & 1 deletion nibabies/workflows/bold/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,6 +209,7 @@
"bold_mask_native",
"cifti_metadata",
"cifti_density",
"bold_rois",
"confounds",
"confounds_metadata",
"goodvoxels_mask",
Expand Down Expand Up @@ -823,12 +824,31 @@
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)

ds_bold_subcortical = pe.Node(

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Added line #L827 was not covered by tests
DerivativesDataSink(
base_directory=output_dir,
suffix="bold",
compress=True,
TaskName=metadata.get("TaskName"),
space="fsLR",
desc="rois",
**timing_parameters,
),
name="ds_bold_subcortical",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)

# fmt: off
workflow.connect([
(inputnode, ds_bold_cifti, [(('bold_cifti', _unlist), 'in_file'),
('source_file', 'source_file'),
('cifti_density', 'density'),
(('cifti_metadata', _read_json), 'meta_dict')])
(('cifti_metadata', _read_json), 'meta_dict')]),
(inputnode, ds_bold_subcortical, [
('bold_rois', 'in_file'),
('source_file', 'source_file')]),

])
# fmt: on

Expand Down
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