diff --git a/nibabies/workflows/anatomical/fit.py b/nibabies/workflows/anatomical/fit.py index 230738ee..8cd72e33 100644 --- a/nibabies/workflows/anatomical/fit.py +++ b/nibabies/workflows/anatomical/fit.py @@ -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') @@ -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, [ @@ -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: @@ -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')]), @@ -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') ]), @@ -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')]), @@ -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']), @@ -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, [ @@ -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: @@ -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')]), @@ -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') ]), @@ -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')]),