Skip to content

FIX: Separate anatomical preproc output from file used for registration #423

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mgxd merged 1 commit into from
Dec 20, 2024
Merged

FIX: Separate anatomical preproc output from file used for registration #423

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 16 additions & 16 deletions nibabies/workflows/anatomical/fit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -189,12 +189,12 @@
)

# Additional buffer if CSF normalization is used
anat_preproc_buffer = pe.Node(
anat_reg_buffer = pe.Node(

Check warning on line 192 in nibabies/workflows/anatomical/fit.py

View check run for this annotation

Codecov / codecov/patch

nibabies/workflows/anatomical/fit.py#L192 

Added line #L192 was not covered by tests
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')

Check warning on line 197 in nibabies/workflows/anatomical/fit.py

View check run for this annotation

Codecov / codecov/patch

nibabies/workflows/anatomical/fit.py#L197 

Added line #L197 was not covered by tests

if reference_anat == 'T1w':
LOGGER.info('ANAT: Using T1w as the reference anatomical')
Expand Down Expand Up @@ -260,7 +260,7 @@
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 @@
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 @@

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 @@
('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 @@
(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 @@
)

# 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 @@
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 @@
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 @@

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 @@
('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 @@
(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
Loading