Disable gzip compression for float NIfTI intermediates (#285)

Author: nx10

src/rbc/core/common.py

@@ -10,13 +10,14 @@
 from typing import TYPE_CHECKING
 
 import nibabel as nib
-from niwrap import afni, fsl
+from niwrap import afni
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from pathlib import Path
 
 from rbc.core.fileops import file_tmp_copy
+from rbc.core.niwrap import generate_exec_folder
 
 __all__ = ["deoblique_and_reorient", "merge_3d_to_4d", "split_4d"]
 
@@ -49,19 +50,24 @@ def deoblique_and_reorient(
 def split_4d(img_4d: Path) -> list[Path]:
     """Split a 4D NIfTI timeseries into individual 3D volumes.
 
+    Volumes are written as uncompressed NIfTI (.nii) to avoid gzip
+    overhead on float intermediates that are read back immediately.
+
     Args:
         img_4d: Path to a 4D NIfTI image.
 
     Returns:
         Sorted list of paths to the individual 3D volume files.
     """
-    split_result = fsl.fslsplit(
-        infile=img_4d, separation_time=True, output_basename="vol_"
-    )
-    assert split_result.out_files is not None  # noqa: S101
-    out_files = split_result.out_files
-    out_dir = out_files[0].parent if isinstance(out_files, list) else out_files.parent
-    return sorted(out_dir.glob("vol_*.nii.gz"))
+    img = nib.nifti1.load(img_4d)
+    volumes = nib.four_to_three(img)
+    out_dir = generate_exec_folder(suffix="split4d")
+    paths: list[Path] = []
+    for idx, vol in enumerate(volumes):
+        out_path = out_dir / f"vol_{idx:04d}.nii"
+        nib.save(vol, out_path)
+        paths.append(out_path)
+    return paths
 
 
 def merge_3d_to_4d(volumes: Sequence[Path], output: Path) -> Path:

src/rbc/core/functional/distortion.py

@@ -349,7 +349,7 @@ def correct_distortion_phasediff(
         diff_img = nib.Nifti1Image(
             diff_data, affine=p1_img.affine, header=p1_img.header
         )
-        phasediff = out_dir / "phasediff.nii.gz"
+        phasediff = out_dir / "phasediff.nii"
         nib.save(diff_img, phasediff)
 
     # 4. Prepare fieldmap (rad/s)
@@ -454,7 +454,7 @@ def correct_distortion_pepolar(
     # 2. Merge forward/reverse into 4D
     merged_path = merge_3d_to_4d(
         volumes=[epi_forward, epi_reverse],
-        output=out_dir / "merged_epi.nii.gz",
+        output=out_dir / "merged_epi.nii",
     )
 
     # 3. Estimate field with TOPUP

src/rbc/core/functional/masking.py

@@ -183,7 +183,7 @@ def bold_masking(
     warped_probseg = ants.ants_apply_transforms(
         reference_image=bold_ref,
         output=ants.ants_apply_transforms_warped_output(
-            warped_output_file_name="probseg_transform.nii.gz"
+            warped_output_file_name="probseg_transform.nii"
         ),
         default_value=0,
         float_=True,
@@ -222,7 +222,7 @@ def bold_masking(
     # mismatches before N4 correction.
     bold_ref_dir_corrected = ants.set_direction_by_matrix(
         infile=bold_ref,
-        outfile="bold_ref_dir_corrected.nii.gz",
+        outfile="bold_ref_dir_corrected.nii",
         direction_matrix=parse_direction_matrix_from_header(
             dilated_binary_mask.output_file
         ),
@@ -233,7 +233,7 @@ def bold_masking(
     n4_bias_correction = ants.n4_bias_field_correction(
         input_image=bold_ref_dir_corrected.outfile,
         output=ants.n4_bias_field_correction_corrected_output(
-            corrected_output_file_name="ref_bold_corrected.nii.gz"
+            corrected_output_file_name="ref_bold_corrected.nii"
         ),
         image_dimensionality=3,
         bspline_fitting=ants.n4_bias_field_correction_bspline_fitting(
@@ -286,7 +286,7 @@ def bold_masking(
         in_file=masked_bold.output_file,
         cl_frac=0.2,
         rbt=[18.3, 65, 90],
-        prefix="uni.nii.gz",
+        prefix="uni.nii",
         t2=True,
     )
 

src/rbc/core/functional/motion.py

@@ -80,7 +80,7 @@ def extract_motion_reference(in_file: Path) -> Path:
             header=ref_im.header,
         )
 
-    temp_slice_file = generate_exec_folder(suffix="motion_ref_input") / "slice.nii.gz"
+    temp_slice_file = generate_exec_folder(suffix="motion_ref_input") / "slice.nii"
     ref_im.to_filename(temp_slice_file)
 
     mc_output_prefix = f"{_MC_PREFIX}_volreg.nii.gz"

src/rbc/core/functional/resampling.py

@@ -99,7 +99,7 @@ def apply_motion_transforms(
             default_value=0,
             dimensionality=3,
             output=ants.ants_apply_transforms_warped_output(
-                f"vol_{idx:04d}_motion.nii.gz"
+                f"vol_{idx:04d}_motion.nii"
             ),
         )
         transformed_vols.append(result.output.output_image_outfile)
@@ -193,7 +193,7 @@ def resample_bold_to_template(
             default_value=0,
             dimensionality=3,
             output=ants.ants_apply_transforms_warped_output(
-                f"vol_{idx:04d}_template.nii.gz"
+                f"vol_{idx:04d}_template.nii"
             ),
         )
         transformed_vols.append(result.output.output_image_outfile)

src/rbc/core/longitudinal/transform.py

@@ -137,7 +137,7 @@ def _transform_4d_chunked(in_file: Path, template: Path, xfm: Path) -> Path:
             dimensionality=3,
             interpolation=ants.ants_apply_transforms_linear(),
             output=ants.ants_apply_transforms_warped_output(
-                f"vol_{idx:04d}_template.nii.gz"
+                f"vol_{idx:04d}_template.nii"
             ),
         )
         transformed_vols.append(result.output.output_image_outfile)