Merge pull request #443 from effigies/rf/anat-template-dimensions

RF: Use genericised "anat" input/output for TemplateDimensions

Author: effigies

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib >= 2.2.0",
     "nibabel >= 4.0.1",
     "nipype >= 1.7.0",
-    "niworkflows >= 1.10.1",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy",
     "packaging",
     "pybids >= 0.11.1",

smriprep/workflows/anatomical.py

@@ -1445,16 +1445,16 @@ def init_anat_template_wf(
 
     # fmt:off
     workflow.connect([
-        (inputnode, anat_ref_dimensions, [('anat_files', 't1w_list')]),
-        (anat_ref_dimensions, denoise, [('t1w_valid_list', 'input_image')]),
+        (inputnode, anat_ref_dimensions, [('anat_files', 'anat_list')]),
+        (anat_ref_dimensions, denoise, [('anat_valid_list', 'input_image')]),
         (anat_ref_dimensions, anat_conform, [
             ('target_zooms', 'target_zooms'),
             ('target_shape', 'target_shape'),
         ]),
         (denoise, anat_conform, [('output_image', 'in_file')]),
         (anat_ref_dimensions, outputnode, [
             ('out_report', 'out_report'),
-            ('t1w_valid_list', 'anat_valid_list'),
+            ('anat_valid_list', 'anat_valid_list'),
         ]),
     ])
     # fmt:on
@@ -1524,7 +1524,7 @@ def _set_threads(in_list, maximum):
 
     # fmt:off
     workflow.connect([
-        (anat_ref_dimensions, anat_conform_xfm, [('t1w_valid_list', 'source_file')]),
+        (anat_ref_dimensions, anat_conform_xfm, [('anat_valid_list', 'source_file')]),
         (anat_conform, anat_conform_xfm, [('out_file', 'target_file')]),
         (anat_conform, n4_correct, [('out_file', 'input_image')]),
         (anat_conform, anat_merge, [