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Merge pull request #423 from mgxd/fix/preproc-normcsf
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FIX: Separate anatomical preproc output from file used for registration
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@mgxd
mgxd authored Dec 20, 2024
2 parents 86264fe + 89df65a commit 7813345
Showing 1 changed file with 16 additions and 16 deletions.
32 changes: 16 additions & 16 deletions nibabies/workflows/anatomical/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,12 +189,12 @@ def init_infant_anat_fit_wf(
)

# Additional buffer if CSF normalization is used
anat_preproc_buffer = pe.Node(
anat_reg_buffer = pe.Node(
niu.IdentityInterface(fields=['anat_preproc']),
name='anat_preproc_buffer',
name='anat_reg_buffer',
)
if not config.workflow.norm_csf:
workflow.connect(anat_buffer, 'anat_preproc', anat_preproc_buffer, 'anat_preproc')
workflow.connect(anat_buffer, 'anat_preproc', anat_reg_buffer, 'anat_preproc')

if reference_anat == 'T1w':
LOGGER.info('ANAT: Using T1w as the reference anatomical')
Expand Down Expand Up @@ -260,7 +260,7 @@ def init_infant_anat_fit_wf(
msm_buffer = pe.Node(niu.IdentityInterface(fields=['sphere_reg_msm']), name='msm_buffer')

workflow.connect([
(anat_preproc_buffer, outputnode, [
(anat_buffer, outputnode, [
('anat_preproc', 'anat_preproc'),
]),
(refined_buffer, outputnode, [
Expand Down Expand Up @@ -929,7 +929,7 @@ def init_infant_anat_fit_wf(
workflow.connect([
(anat_buffer, csf_norm_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(seg_buffer, csf_norm_wf, [('anat_tpms', 'inputnode.anat_tpms')]),
(csf_norm_wf, anat_preproc_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
(csf_norm_wf, anat_reg_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
]) # fmt:skip

if templates:
Expand All @@ -947,7 +947,7 @@ def init_infant_anat_fit_wf(

workflow.connect([
(inputnode, register_template_wf, [('roi', 'inputnode.lesion_mask')]),
(anat_preproc_buffer, register_template_wf, [
(anat_reg_buffer, register_template_wf, [
('anat_preproc', 'inputnode.moving_image'),
]),
(refined_buffer, register_template_wf, [('anat_mask', 'inputnode.moving_mask')]),
Expand Down Expand Up @@ -991,7 +991,7 @@ def init_infant_anat_fit_wf(
('anat2std_xfm', 'inputnode.anat2std_xfm'),
('std2anat_xfm', 'inputnode.std2anat_xfm'),
]),
(anat_preproc_buffer, concat_reg_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(anat_buffer, concat_reg_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(sourcefile_buffer, ds_concat_reg_wf, [
('anat_source_files', 'inputnode.source_files')
]),
Expand Down Expand Up @@ -1184,7 +1184,7 @@ def init_infant_anat_fit_wf(
(seg_buffer, refinement_wf, [
('ants_segs', 'inputnode.ants_segs'), # TODO: Verify this is the same as dseg
]),
(anat_preproc_buffer, applyrefined, [('anat_preproc', 'in_file')]),
(anat_buffer, applyrefined, [('anat_preproc', 'in_file')]),
(refinement_wf, applyrefined, [('outputnode.out_brainmask', 'in_mask')]),
(refinement_wf, refined_buffer, [('outputnode.out_brainmask', 'anat_mask')]),
(applyrefined, refined_buffer, [('out_file', 'anat_brain')]),
Expand Down Expand Up @@ -1463,12 +1463,12 @@ def init_infant_single_anat_fit_wf(
)

# Additional buffer if CSF normalization is used
anat_preproc_buffer = pe.Node(
anat_reg_buffer = pe.Node(
niu.IdentityInterface(fields=['anat_preproc']),
name='anat_preproc_buffer',
name='anat_reg_buffer',
)
if not config.workflow.norm_csf:
workflow.connect(anat_buffer, 'anat_preproc', anat_preproc_buffer, 'anat_preproc')
workflow.connect(anat_buffer, 'anat_preproc', anat_reg_buffer, 'anat_preproc')

aseg_buffer = pe.Node(
niu.IdentityInterface(fields=['anat_aseg']),
Expand Down Expand Up @@ -1509,7 +1509,7 @@ def init_infant_single_anat_fit_wf(
msm_buffer = pe.Node(niu.IdentityInterface(fields=['sphere_reg_msm']), name='msm_buffer')

workflow.connect([
(anat_preproc_buffer, outputnode, [
(anat_buffer, outputnode, [
('anat_preproc', 'anat_preproc'),
]),
(refined_buffer, outputnode, [
Expand Down Expand Up @@ -1846,7 +1846,7 @@ def init_infant_single_anat_fit_wf(
workflow.connect([
(anat_buffer, csf_norm_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(seg_buffer, csf_norm_wf, [('anat_tpms', 'inputnode.anat_tpms')]),
(csf_norm_wf, anat_preproc_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
(csf_norm_wf, anat_reg_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
]) # fmt:skip

if templates:
Expand All @@ -1864,7 +1864,7 @@ def init_infant_single_anat_fit_wf(

workflow.connect([
(inputnode, register_template_wf, [('roi', 'inputnode.lesion_mask')]),
(anat_preproc_buffer, register_template_wf, [
(anat_reg_buffer, register_template_wf, [
('anat_preproc', 'inputnode.moving_image'),
]),
(refined_buffer, register_template_wf, [('anat_mask', 'inputnode.moving_mask')]),
Expand Down Expand Up @@ -1909,7 +1909,7 @@ def init_infant_single_anat_fit_wf(
('anat2std_xfm', 'inputnode.anat2std_xfm'),
('std2anat_xfm', 'inputnode.std2anat_xfm'),
]),
(anat_preproc_buffer, concat_reg_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(anat_buffer, concat_reg_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
(sourcefile_buffer, ds_concat_reg_wf, [
('anat_source_files', 'inputnode.source_files')
]),
Expand Down Expand Up @@ -2091,7 +2091,7 @@ def init_infant_single_anat_fit_wf(
(seg_buffer, refinement_wf, [
('ants_segs', 'inputnode.ants_segs'),
]),
(anat_preproc_buffer, applyrefined, [('anat_preproc', 'in_file')]),
(anat_buffer, applyrefined, [('anat_preproc', 'in_file')]),
(refinement_wf, applyrefined, [('outputnode.out_brainmask', 'in_mask')]),
(refinement_wf, refined_buffer, [('outputnode.out_brainmask', 'anat_mask')]),
(applyrefined, refined_buffer, [('out_file', 'anat_brain')]),
Expand Down

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