fix bugs for sessions

khanlab · Apr 26, 2023 · 5a1a1d0 · 5a1a1d0
1 parent f76d252
commit 5a1a1d0
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/scattr/workflow/rules/freesurfer.smk b/scattr/workflow/rules/freesurfer.smk
@@ -67,9 +67,13 @@ rule thalamic_segmentation:
         fs_license=fs_license,
     output:
         thal_seg=str(
-            Path(freesurfer_dir)
-            / "sub-{subject}/mri/ThalamicNuclei.v12.T1.mgz"
-        ),
+            Path(
+                bids(
+                    root=freesurfer_dir,
+                    **inputs.subj_wildcards
+                )
+            ).parent / "mri" / "ThalamicNuclei.v12.T1.mgz"
+        )
     threads: 4
     resources:
         mem_mb=16000,
@@ -99,8 +103,13 @@ rule mgz2nii:
         if not config.get("skip_thal_seg")
         else [],
         aparcaseg=str(
-            Path(freesurfer_dir) / "sub-{subject}/mri/aparc+aseg.mgz"
-        ),
+            Path(
+                bids(
+                    root=freesurfer_dir,
+                    **inputs.subj_wildcards
+                )
+            ).parent / "mri" / "aparc+aseg.mgz"
+        )
     params:
         freesurfer_dir=freesurfer_dir,
         fs_license=fs_license,

diff --git a/scattr/workflow/rules/mrtpipelines.smk b/scattr/workflow/rules/mrtpipelines.smk
@@ -168,7 +168,6 @@ rule responsemean:
     input:
         subject_rf=expand(
             bids_response_out(
-                subject="{subject}",
                 desc="{tissue}",
             ),
             zip,