Faster quasiraw pipeline + mask interpolation fix

brainprep/interfaces/ants.py

@@ -71,7 +71,7 @@ def biasfield(
         "N4BiasFieldCorrection",
         "-d", "3",
         "-i", str(image_file),
-        "-s", "1",
+        "-s", "4",
         "-b", "[1x1x1,3]",
         "-c", "[50x50x50x50,0.001]",
         "-t", "[0.15,0.01,200]",

brainprep/interfaces/fsl.py

@@ -201,7 +201,8 @@ def scale(
         image_file: File,
         scale: int,
         output_dir: Directory,
-        entities: dict) -> tuple[list[str], tuple[File]]:
+        entities: dict,
+        interp: str | None = None) -> tuple[list[str], tuple[File]]:
     """
     Apply an isotropic resampling transformation to a BIDS-compliant image
     file using FSL's `flirt`.
@@ -216,6 +217,10 @@ def scale(
         Directory where the scaled image will be saved.
     entities : dict
         A dictionary of parsed BIDS entities including modality.
+    interp : str, default=None
+        Interpolation method used by `flirt`. One of "trilinear",
+        "nearestneighbour", "sinc" or "spline". If None, `flirt`'s
+        default ("trilinear") is used.
 
     Returns
     -------
@@ -239,6 +244,10 @@ def scale(
         "-omat", str(transform_file),
         "-verbose", "1",
     ]
+    if interp is not None:
+        command += [
+            "-interp", interp
+        ]
 
     return command, (scaled_anatomical_file, transform_file)
 
@@ -296,6 +305,9 @@ def affine(
         "-bins", "256",
         "-interp", "trilinear",
         "-dof", "9",
+        "-searchrx", "-30", "30",
+        "-searchry", "-30", "30",
+        "-searchrz", "-30", "30",
         "-out", str(aligned_anatomical_file),
         "-omat", str(transform_file),
         "-verbose", "1"

brainprep/workflow/quasiraw.py

@@ -172,6 +172,7 @@ def brainprep_quasiraw(
         1,
         workspace_dir / "05-scale",
         entities,
+        interp="nearestneighbour"
     )
     bc_anatomical_file, _ = interfaces.biasfield(
         scaled_anatomical_file,