Merge pull request #333 from mgxd/fix/multi-run-connections

FIX: Multiple T2ws, coerce reference to string

Author: mgxd

nibabies/workflows/anatomical/base.py

@@ -285,7 +285,8 @@ def init_infant_anat_wf(
 
         (t2w_template_wf, t2w_preproc_wf, [("outputnode.anat_ref", "inputnode.in_anat")]),
         (t2w_template_wf, anat_derivatives_wf, [
-            ("outputnode.anat_valid_list", "inputnode.t2w_source_files")]),
+            ("outputnode.anat_valid_list", "inputnode.t2w_source_files"),
+            ("outputnode.anat_realign_xfm", "inputnode.t2w_ref_xfms")]),
 
         (t1w_preproc_wf, coregistration_wf, [("outputnode.anat_preproc", "inputnode.in_t1w")]),
         (t1w_preproc_wf, coreg_report_wf, [("outputnode.anat_preproc", "inputnode.t1w_preproc")]),

nibabies/workflows/anatomical/template.py

@@ -274,7 +274,7 @@ def init_anat_template_wf(
             (anat_reorient, applyxfm_aseg, [('out_file', 'reference_image')]),
             (aseg_xfm, applyxfm_aseg, [('out', 'transforms')]),
             (applyxfm_aseg, aseg_reorient, [('output_image', 'in_file')]),
-            (applyxfm_aseg, outputnode, [('out_file', 'anat_aseg')]),
+            (aseg_reorient, outputnode, [('out_file', 'anat_aseg')]),
         ])
         # fmt:on
 
@@ -305,4 +305,4 @@ def _set_threads(in_list, maximum):
 
 
 def get_reference(anatomicals: list, anat_reference: str) -> int:
-    return anatomicals.index(anat_reference)
+    return anatomicals.index(str(anat_reference))