Bug fixes to anatomical workflow (#40)

* Fix output path of composite warp
* Fix fslmaths parameters since niwrap update"
* Inline renaming of anatomical files

Author: kaitj

src/rbc/core/anatomical/registration.py

@@ -144,4 +144,6 @@ def ants_registration(
             print_out_composite_warp_file=True,
         ),
     )
-    return SimpleNamespace(forward=fwd.output, inverse=rev.output)
+    return SimpleNamespace(
+        forward=fwd.output.output_image_outfile, inverse=rev.output.output_image_outfile
+    )

src/rbc/core/anatomical/segmentation.py

@@ -53,8 +53,8 @@ def fsl_tissue_segmentation(in_file: Path, output_prefix: str) -> SimpleNamespac
         tissue_type: fsl.fslmaths(
             input_files=[tissues.root / f"{output_prefix}_pve_{idx}.nii.gz"],
             operations=[
-                fsl.fslmaths_operation(thr=0.95),
-                fsl.fslmaths_operation(bin_=True),
+                fsl.fslmaths_operation_thr(thr=0.95),
+                fsl.fslmaths_operation_bin(bin_=True),
             ],
             output=f"{tissue_type}_mask.nii.gz",
         ).output_file

src/rbc/workflows/anatomical.py

@@ -42,16 +42,15 @@ def single_session(in_t1w: Path, output_dir: Path) -> None:
     )
 
     # Prep files to save
-    t1w_outputs = [
-        (extracted_t1w.brain_extracted_image, "brain", "T1w"),
-        (extracted_t1w.brain_mask, "T1w", "mask"),
-        (tissue_masks.csf, "csf", "mask"),
-        (tissue_masks.gm, "gm", "mask"),
-        (tissue_masks.wm, "wm", "mask"),
-    ]
     renamed_files = [
         rename(out_file, bids(desc=desc, suffix=suffix, ext=".nii.gz"))
-        for out_file, desc, suffix in t1w_outputs
+        for out_file, desc, suffix in [
+            (extracted_t1w.brain_extracted_image, "brain", "T1w"),
+            (extracted_t1w.brain_mask, "T1w", "mask"),
+            (tissue_masks.csf, "csf", "mask"),
+            (tissue_masks.gm, "gm", "mask"),
+            (tissue_masks.wm, "wm", "mask"),
+        ]
     ]
     niwrap_helper.save(
         [*renamed_files, transforms.forward, transforms.inverse],