Merge remote-tracking branch 'upstream/master' into fsaverage-reg-sphere

Author: tsalo

smriprep/workflows/anatomical.py

@@ -61,10 +61,10 @@
 from .fit.registration import init_register_template_wf
 from .outputs import (
     init_anat_reports_wf,
-    init_anat_second_derivatives_wf,
     init_ds_anat_volumes_wf,
     init_ds_dseg_wf,
     init_ds_fs_registration_wf,
+    init_ds_fs_segs_wf,
     init_ds_grayord_metrics_wf,
     init_ds_mask_wf,
     init_ds_surface_metrics_wf,
@@ -287,7 +287,6 @@ def init_anat_preproc_wf(
     ds_std_volumes_wf = init_ds_anat_volumes_wf(
         bids_root=bids_root,
         output_dir=output_dir,
-        name='ds_std_volumes_wf',
     )
 
     workflow.connect([
@@ -320,10 +319,10 @@ def init_anat_preproc_wf(
         ]),
         (anat_fit_wf, ds_std_volumes_wf, [
             ('outputnode.t1w_valid_list', 'inputnode.source_files'),
-            ('outputnode.t1w_preproc', 'inputnode.t1w_preproc'),
-            ('outputnode.t1w_mask', 'inputnode.t1w_mask'),
-            ('outputnode.t1w_dseg', 'inputnode.t1w_dseg'),
-            ('outputnode.t1w_tpms', 'inputnode.t1w_tpms'),
+            ('outputnode.t1w_preproc', 'inputnode.anat_preproc'),
+            ('outputnode.t1w_mask', 'inputnode.anat_mask'),
+            ('outputnode.t1w_dseg', 'inputnode.anat_dseg'),
+            ('outputnode.t1w_tpms', 'inputnode.anat_tpms'),
         ]),
         (template_iterator_wf, ds_std_volumes_wf, [
             ('outputnode.std_t1w', 'inputnode.ref_file'),
@@ -335,17 +334,12 @@ def init_anat_preproc_wf(
     ])  # fmt:skip
 
     if freesurfer:
-        anat_second_derivatives_wf = init_anat_second_derivatives_wf(
+        ds_fs_segs_wf = init_ds_fs_segs_wf(
             bids_root=bids_root,
             output_dir=output_dir,
-            cifti_output=cifti_output,
-        )
-        surface_derivatives_wf = init_surface_derivatives_wf(
-            cifti_output=cifti_output,
-        )
-        ds_surfaces_wf = init_ds_surfaces_wf(
-            bids_root=bids_root, output_dir=output_dir, surfaces=['inflated']
         )
+        surface_derivatives_wf = init_surface_derivatives_wf()
+        ds_surfaces_wf = init_ds_surfaces_wf(output_dir=output_dir, surfaces=['inflated'])
         ds_curv_wf = init_ds_surface_metrics_wf(
             bids_root=bids_root, output_dir=output_dir, metrics=['curv'], name='ds_curv_wf'
         )
@@ -355,7 +349,7 @@ def init_anat_preproc_wf(
                 ('outputnode.t1w_preproc', 'inputnode.reference'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 ('outputnode.subject_id', 'inputnode.subject_id'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
+                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (anat_fit_wf, ds_surfaces_wf, [
                 ('outputnode.t1w_valid_list', 'inputnode.source_files'),
@@ -369,12 +363,12 @@ def init_anat_preproc_wf(
             (surface_derivatives_wf, ds_curv_wf, [
                 ('outputnode.curv', 'inputnode.curv'),
             ]),
-            (anat_fit_wf, anat_second_derivatives_wf, [
+            (anat_fit_wf, ds_fs_segs_wf, [
                 ('outputnode.t1w_valid_list', 'inputnode.source_files'),
             ]),
-            (surface_derivatives_wf, anat_second_derivatives_wf, [
-                ('outputnode.out_aseg', 'inputnode.t1w_fs_aseg'),
-                ('outputnode.out_aparc', 'inputnode.t1w_fs_aparc'),
+            (surface_derivatives_wf, ds_fs_segs_wf, [
+                ('outputnode.out_aseg', 'inputnode.anat_fs_aseg'),
+                ('outputnode.out_aparc', 'inputnode.anat_fs_aparc'),
             ]),
             (surface_derivatives_wf, outputnode, [
                 ('outputnode.out_aseg', 't1w_aseg'),
@@ -765,10 +759,12 @@ def init_anat_fit_wf(
             longitudinal=longitudinal,
             omp_nthreads=omp_nthreads,
             num_files=num_t1w,
-            contrast='T1w',
+            image_type='T1w',
             name='anat_template_wf',
         )
-        ds_template_wf = init_ds_template_wf(output_dir=output_dir, num_t1w=num_t1w)
+        ds_template_wf = init_ds_template_wf(
+            output_dir=output_dir, num_anat=num_t1w, image_type='T1w'
+        )
 
         # fmt:off
         workflow.connect([
@@ -781,11 +777,11 @@ def init_anat_fit_wf(
                 ('outputnode.out_report', 'inputnode.t1w_conform_report'),
             ]),
             (anat_template_wf, ds_template_wf, [
-                ('outputnode.anat_realign_xfm', 'inputnode.t1w_ref_xfms'),
+                ('outputnode.anat_realign_xfm', 'inputnode.anat_ref_xfms'),
             ]),
             (sourcefile_buffer, ds_template_wf, [('source_files', 'inputnode.source_files')]),
-            (t1w_buffer, ds_template_wf, [('t1w_preproc', 'inputnode.t1w_preproc')]),
-            (ds_template_wf, outputnode, [('outputnode.t1w_preproc', 't1w_preproc')]),
+            (t1w_buffer, ds_template_wf, [('t1w_preproc', 'inputnode.anat_preproc')]),
+            (ds_template_wf, outputnode, [('outputnode.anat_preproc', 't1w_preproc')]),
         ])
         # fmt:on
     else:
@@ -954,16 +950,16 @@ def init_anat_fit_wf(
             workflow.connect([
                 (fast, lut_t1w_dseg, [('partial_volume_map', 'in_dseg')]),
                 (sourcefile_buffer, ds_dseg_wf, [('source_files', 'inputnode.source_files')]),
-                (lut_t1w_dseg, ds_dseg_wf, [('out', 'inputnode.t1w_dseg')]),
-                (ds_dseg_wf, seg_buffer, [('outputnode.t1w_dseg', 't1w_dseg')]),
+                (lut_t1w_dseg, ds_dseg_wf, [('out', 'inputnode.anat_dseg')]),
+                (ds_dseg_wf, seg_buffer, [('outputnode.anat_dseg', 't1w_dseg')]),
             ])
         if not have_tpms:
             ds_tpms_wf = init_ds_tpms_wf(output_dir=output_dir)
             workflow.connect([
                 (fast, fast2bids, [('partial_volume_files', 'inlist')]),
                 (sourcefile_buffer, ds_tpms_wf, [('source_files', 'inputnode.source_files')]),
-                (fast2bids, ds_tpms_wf, [('out', 'inputnode.t1w_tpms')]),
-                (ds_tpms_wf, seg_buffer, [('outputnode.t1w_tpms', 't1w_tpms')]),
+                (fast2bids, ds_tpms_wf, [('out', 'inputnode.anat_tpms')]),
+                (ds_tpms_wf, seg_buffer, [('outputnode.anat_tpms', 't1w_tpms')]),
             ])
         # fmt:on
     else:
@@ -998,7 +994,9 @@ def init_anat_fit_wf(
             omp_nthreads=omp_nthreads,
             templates=templates,
         )
-        ds_template_registration_wf = init_ds_template_registration_wf(output_dir=output_dir)
+        ds_template_registration_wf = init_ds_template_registration_wf(
+            output_dir=output_dir, image_type='T1w'
+        )
 
         # fmt:off
         workflow.connect([
@@ -1081,17 +1079,17 @@ def init_anat_fit_wf(
 
     fsnative_xfms = precomputed.get('transforms', {}).get('fsnative')
     if not fsnative_xfms:
-        ds_fs_registration_wf = init_ds_fs_registration_wf(output_dir=output_dir)
+        ds_fs_registration_wf = init_ds_fs_registration_wf(output_dir=output_dir, image_type='T1w')
         # fmt:off
         workflow.connect([
             (sourcefile_buffer, ds_fs_registration_wf, [
                 ('source_files', 'inputnode.source_files'),
             ]),
             (surface_recon_wf, ds_fs_registration_wf, [
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
+                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (ds_fs_registration_wf, outputnode, [
-                ('outputnode.fsnative2t1w_xfm', 'fsnative2t1w_xfm'),
+                ('outputnode.fsnative2anat_xfm', 'fsnative2t1w_xfm'),
             ]),
         ])
         # fmt:on
@@ -1114,7 +1112,7 @@ def init_anat_fit_wf(
             (surface_recon_wf, refinement_wf, [
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 ('outputnode.subject_id', 'inputnode.subject_id'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
+                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (t1w_buffer, refinement_wf, [
                 ('t1w_preproc', 'inputnode.reference_image'),
@@ -1135,7 +1133,7 @@ def init_anat_fit_wf(
             longitudinal=longitudinal,
             omp_nthreads=omp_nthreads,
             num_files=len(t2w),
-            contrast='T2w',
+            image_type='T2w',
             name='t2w_template_wf',
         )
         bbreg = pe.Node(
@@ -1216,15 +1214,13 @@ def init_anat_fit_wf(
         LOGGER.info(f'ANAT Stage 8: Creating GIFTI surfaces for {surfs + spheres}')
     if surfs:
         gifti_surfaces_wf = init_gifti_surfaces_wf(surfaces=surfs)
-        ds_surfaces_wf = init_ds_surfaces_wf(
-            bids_root=bids_root, output_dir=output_dir, surfaces=surfs
-        )
+        ds_surfaces_wf = init_ds_surfaces_wf(output_dir=output_dir, surfaces=surfs)
         # fmt:off
         workflow.connect([
             (surface_recon_wf, gifti_surfaces_wf, [
                 ('outputnode.subject_id', 'inputnode.subject_id'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
+                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (gifti_surfaces_wf, surfaces_buffer, [
                 (f'outputnode.{surf}', surf) for surf in surfs
@@ -1240,7 +1236,7 @@ def init_anat_fit_wf(
             surfaces=spheres, to_scanner=False, name='gifti_spheres_wf'
         )
         ds_spheres_wf = init_ds_surfaces_wf(
-            bids_root=bids_root, output_dir=output_dir, surfaces=spheres, name='ds_spheres_wf'
+            output_dir=output_dir, surfaces=spheres, name='ds_spheres_wf'
         )
         # fmt:off
         workflow.connect([
@@ -1316,7 +1312,6 @@ def init_anat_fit_wf(
         LOGGER.info('ANAT Stage 9: Creating fsLR registration sphere')
         fsLR_reg_wf = init_fsLR_reg_wf()
         ds_fsLR_reg_wf = init_ds_surfaces_wf(
-            bids_root=bids_root,
             output_dir=output_dir,
             surfaces=['sphere_reg_fsLR'],
             name='ds_fsLR_reg_wf',
@@ -1341,7 +1336,6 @@ def init_anat_fit_wf(
         LOGGER.info('ANAT Stage 10: Creating MSM-Sulc registration sphere')
         msm_sulc_wf = init_msm_sulc_wf(sloppy=sloppy)
         ds_msmsulc_wf = init_ds_surfaces_wf(
-            bids_root=bids_root,
             output_dir=output_dir,
             surfaces=['sphere_reg_msm'],
             name='ds_msmsulc_wf',
@@ -1375,7 +1369,7 @@ def init_anat_template_wf(
     longitudinal: bool,
     omp_nthreads: int,
     num_files: int,
-    contrast: str,
+    image_type: ty.Literal['T1w', 'T2w'],
     name: str = 'anat_template_wf',
 ):
     """
@@ -1388,7 +1382,7 @@ def init_anat_template_wf(
 
             from smriprep.workflows.anatomical import init_anat_template_wf
             wf = init_anat_template_wf(
-                longitudinal=False, omp_nthreads=1, num_files=1, contrast="T1w"
+                longitudinal=False, omp_nthreads=1, num_files=1, image_type="T1w"
             )
 
     Parameters
@@ -1400,8 +1394,8 @@ def init_anat_template_wf(
         Maximum number of threads an individual process may use
     num_files : :obj:`int`
         Number of images
-    contrast : :obj:`str`
-        Name of contrast, for reporting purposes, e.g., T1w, T2w, PDw
+    image_type : :obj:`str`
+       MR image type (T1w, T2w, etc.)
     name : :obj:`str`, optional
         Workflow name (default: anat_template_wf)
 
@@ -1427,8 +1421,8 @@ def init_anat_template_wf(
     if num_files > 1:
         fs_ver = fs.Info().looseversion() or '(version unknown)'
         workflow.__desc__ = f"""\
-An anatomical {contrast}-reference map was computed after registration of
-{num_files} {contrast} images (after INU-correction) using
+An anatomical {image_type}-reference map was computed after registration of
+{num_files} {image} images (after INU-correction) using
 `mri_robust_template` [FreeSurfer {fs_ver}, @fs_template].
 """