fix rename in utils and keep only txt params file

Author: jpillai00

src/rbc/core/utils.py

@@ -47,11 +47,10 @@ def get_base_entities(
 
 def rename(in_file: str | Path, new_name: str | Path) -> Path:
     """Rename a file, keeping it in the same directory."""
-    in_file = Path(in_file)
-    new_path = in_file.with_name(Path(new_name).name)
-    if new_path.exists():
-        raise FileExistsError(f"Target file already exists: {new_path}")
-    return in_file.rename(new_path)
+    target = in_file.with_name(new_name)
+    if in_file == target:
+        return in_file
+    return Path(shutil.move(str(in_file), str(target)))
 
 def save_directory(in_dir: str | Path, out_dir: str | Path, name: str) -> Path:
     """Save a directory by copying it to a new location.

src/rbc/workflows/functional.py

@@ -56,7 +56,6 @@ def single_session(in_bold: Path, output_dir: Path, start_tr: int = 2) -> None:
         (motion_reference.output_file, None, "sbref", ".nii.gz"),
         (motion_corrected.bold.with_suffix(".nii.gz"), "motion", "bold", ".nii.gz"),
         (motion_corrected.par, "motionParams", "motion", ".txt"),
-        (motion_corrected.par, "movementParameters", "motion", ".1D"),
         (motion_corrected.rms_rel, "relsDisplacement", "motion", ".rms"),
         (motion_corrected.rms_abs, "maxDisplacement", "motion", ".rms"),
     ]
@@ -71,7 +70,7 @@ def single_session(in_bold: Path, output_dir: Path, start_tr: int = 2) -> None:
         rename(
             out_file,
             bids(desc=desc, suffix=suffix, ext=ext)
-            if desc
+            if desc is not None
             else bids(suffix=suffix, ext=ext),
         )
         for out_file, desc, suffix, ext in outputs