junifer 0.0.8.dev329__tar.gz → 0.0.8.dev335__tar.gz

{junifer-0.0.8.dev329/junifer.egg-info → junifer-0.0.8.dev335}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev329
+Version: 0.0.8.dev335
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.8.dev335/docs/changes/newsfragments/530.change

@@ -0,0 +1 @@
+Use single precision in ``antsApplyTransforms`` (``--float 1``), halving its memory and giving float32 instead of float64 data, with differences below 0.002% of the data range by `Fede Raimondo`_

junifer-0.0.8.dev335/docs/changes/newsfragments/530.enh

@@ -0,0 +1 @@
+Warp the volumes of 4D data in chunks of ``preprocessing.warping.chunksize`` volumes (default 100) in :class:`.SpaceWarper`, as the memory used by ANTs and FSL grows with the number of volumes (e.g., about 53 GB to warp 1200 volumes to native space with ANTs) by `Fede Raimondo`_

junifer-0.0.8.dev335/docs/changes/newsfragments/530.enh.1

@@ -0,0 +1 @@
+Write the intermediate images (e.g., the warped, smoothed or filtered data) uncompressed in the temporary directory of the element, as they are read right away and deleted after the element is processed, so there is no need to spend time compressing and decompressing them, and run the FSL commands with ``FSLOUTPUTTYPE=NIFTI`` to write them uncompressed by `Fede Raimondo`_

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/docs/using/configuring.rst

@@ -63,3 +63,9 @@ Available Configurations
      - ``preprocessing.dump.granularity``
      - "full" or "final"
      - Dump all pre-processing steps or just the final pre-processed data
+   * - ``JUNIFER_PREPROCESSING_WARPING_CHUNKSIZE``
+     - ``preprocessing.warping.chunksize``
+     - int
+     - | Number of volumes of 4D data to warp at once with
+       | :class:`.SpaceWarper` (default 100). The memory used by ANTs and FSL
+       | grows with the number of volumes, so smaller chunks use less memory

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev329'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev329')
+__version__ = version = '0.0.8.dev335'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev335')
 
-__commit_id__ = commit_id = 'g33802e12a'
+__commit_id__ = commit_id = 'g611612030'

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/api/res/fsl/run_fsl_docker.sh

@@ -34,6 +34,10 @@ echo "Docker args: ${docker_args[*]}" >&2
 echo "Corrected args for FSL: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
+# Pass the output type, as FSL writes it instead of the type of the extension
+if [ -n "${FSLOUTPUTTYPE}" ]; then
+    docker_args+=("-e FSLOUTPUTTYPE=${FSLOUTPUTTYPE}")
+fi
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"
 echo "Running command: ${cmd}" >&2
 ${cmd}

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/maps/_ants_maps_warper.py

@@ -100,16 +100,17 @@ class ANTsMapsWarper:
             logger.debug("Using ANTs for maps transformation")
 
             # Save existing maps image to a tempfile
-            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
             nib.save(maps_img, prewarp_maps_path)
 
             # Create a tempfile for warped output
-            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            warped_maps_path = element_tempdir / "maps_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n LanczosWindowedSinc",
                 f"-i {prewarp_maps_path.resolve()}",
                 # use resampled reference
@@ -133,20 +134,21 @@ class ANTsMapsWarper:
                 extra_input=None,
             )
             # Save template to a tempfile
-            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii"
             nib.save(template_space_img, template_space_img_path)
 
             # Save existing maps image to a tempfile
-            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
             nib.save(maps_img, prewarp_maps_path)
 
             # Create a tempfile for warped output
-            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            warped_maps_path = element_tempdir / "maps_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n LanczosWindowedSinc",
                 f"-i {prewarp_maps_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/maps/_fsl_maps_warper.py

@@ -66,13 +66,14 @@ class FSLMapsWarper:
         )
 
         # Save existing maps image to a tempfile
-        prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+        prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
         nib.save(maps_img, prewarp_maps_path)
 
         # Create a tempfile for warped output
-        warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+        warped_maps_path = element_tempdir / "maps_warped.nii"
         # Set applywarp command
         applywarp_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "applywarp",
             "--interp=spline",
             f"-i {prewarp_maps_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/masks/_ants_mask_warper.py

@@ -121,16 +121,17 @@ class ANTsMaskWarper:
             logger.debug("Using ANTs for mask transformation")
 
             # Save existing mask image to a tempfile
-            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
             nib.save(mask_img, prewarp_mask_path)
 
             # Create a tempfile for warped output
-            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            warped_mask_path = element_tempdir / "mask_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
@@ -154,20 +155,21 @@ class ANTsMaskWarper:
                 extra_input=None,
             )
             # Save template to a tempfile
-            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii"
             nib.save(template_space_img, template_space_img_path)
 
             # Save existing mask image to a tempfile
-            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
             nib.save(mask_img, prewarp_mask_path)
 
             # Create a tempfile for warped output
-            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            warped_mask_path = element_tempdir / "mask_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 f"-n {_get_interpolation_method(mask_img)}",
                 f"-i {prewarp_mask_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/masks/_fsl_mask_warper.py

@@ -87,13 +87,14 @@ class FSLMaskWarper:
         )
 
         # Save existing mask image to a tempfile
-        prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+        prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
         nib.save(mask_img, prewarp_mask_path)
 
         # Create a tempfile for warped output
-        warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+        warped_mask_path = element_tempdir / "mask_warped.nii"
         # Set applywarp command
         applywarp_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "applywarp",
             f"--interp={_get_interpolation_method(mask_img)}",
             f"-i {prewarp_mask_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/parcellations/_ants_parcellation_warper.py

@@ -101,19 +101,20 @@ class ANTsParcellationWarper:
 
             # Save existing parcellation image to a tempfile
             prewarp_parcellation_path = (
-                element_tempdir / "prewarp_parcellation.nii.gz"
+                element_tempdir / "prewarp_parcellation.nii"
             )
             nib.save(parcellation_img, prewarp_parcellation_path)
 
             # Create a tempfile for warped output
             warped_parcellation_path = (
-                element_tempdir / "parcellation_warped.nii.gz"
+                element_tempdir / "parcellation_warped.nii"
             )
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_parcellation_path.resolve()}",
                 # use resampled reference
@@ -139,24 +140,25 @@ class ANTsParcellationWarper:
                 extra_input=None,
             )
             # Save template to a tempfile
-            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii"
             nib.save(template_space_img, template_space_img_path)
 
             # Save existing parcellation image to a tempfile
             prewarp_parcellation_path = (
-                element_tempdir / "prewarp_parcellation.nii.gz"
+                element_tempdir / "prewarp_parcellation.nii"
             )
             nib.save(parcellation_img, prewarp_parcellation_path)
 
             # Create a tempfile for warped output
             warped_parcellation_path = (
-                element_tempdir / "parcellation_warped.nii.gz"
+                element_tempdir / "parcellation_warped.nii"
             )
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_parcellation_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -67,16 +67,15 @@ class FSLParcellationWarper:
 
         # Save existing parcellation image to a tempfile
         prewarp_parcellation_path = (
-            element_tempdir / "prewarp_parcellation.nii.gz"
+            element_tempdir / "prewarp_parcellation.nii"
         )
         nib.save(parcellation_img, prewarp_parcellation_path)
 
         # Create a tempfile for warped output
-        warped_parcellation_path = (
-            element_tempdir / "parcellation_warped.nii.gz"
-        )
+        warped_parcellation_path = element_tempdir / "parcellation_warped.nii"
         # Set applywarp command
         applywarp_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "applywarp",
             "--interp=nn",
             f"-i {prewarp_parcellation_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/markers/falff/_junifer_falff.py

@@ -137,8 +137,8 @@ class JuniferALFF(metaclass=Singleton):
         element_tempdir = WorkDirManager().get_element_tempdir(
             prefix="junifer_lff"
         )
-        output_alff_path = element_tempdir / "output_alff.nii.gz"
-        output_falff_path = element_tempdir / "output_falff.nii.gz"
+        output_alff_path = element_tempdir / "output_alff.nii"
+        output_falff_path = element_tempdir / "output_falff.nii"
         # Save computed data to file
         nib.save(alff_data, output_alff_path)
         nib.save(falff_data, output_falff_path)

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/markers/reho/_junifer_reho.py

@@ -204,7 +204,7 @@ class JuniferReHo(metaclass=Singleton):
         element_tempdir = WorkDirManager().get_element_tempdir(
             prefix="junifer_reho"
         )
-        output_path = element_tempdir / "output.nii.gz"
+        output_path = element_tempdir / "output.nii"
         # Save computed data to file
         nib.save(output_data, output_path)
 

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/_temporal_filter.py

@@ -151,7 +151,7 @@ class TemporalFilter(BasePreprocessor):
                 extra_input=extra_input,
             )
             # Save generated mask for use later
-            generated_mask_img_path = element_tempdir / "generated_mask.nii.gz"
+            generated_mask_img_path = element_tempdir / "generated_mask.nii"
             nib.save(mask_img, generated_mask_img_path)
 
             # Save BOLD mask and link it to the BOLD data type dict;
@@ -193,7 +193,7 @@ class TemporalFilter(BasePreprocessor):
         # Fix t_r as nilearn messes it up
         cleaned_img.header["pixdim"][4] = t_r
         # Save filtered data
-        filtered_data_path = element_tempdir / "filtered_data.nii.gz"
+        filtered_data_path = element_tempdir / "filtered_data.nii"
         nib.save(cleaned_img, filtered_data_path)
 
         logger.debug("Updating `BOLD`")

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/_temporal_slicer.py

@@ -151,7 +151,7 @@ class TemporalSlicer(BasePreprocessor):
         # Fix t_r as nilearn messes it up
         sliced_img.header["pixdim"][4] = t_r
         # Save sliced data
-        sliced_img_path = element_tempdir / "sliced_data.nii.gz"
+        sliced_img_path = element_tempdir / "sliced_data.nii"
         nib.save(sliced_img, sliced_img_path)
 
         logger.debug("Updating `BOLD`")

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -620,7 +620,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
                 extra_input=extra_input,
             )
             # Save generated mask for use later
-            generated_mask_img_path = element_tempdir / "generated_mask.nii.gz"
+            generated_mask_img_path = element_tempdir / "generated_mask.nii"
             nib.save(mask_img, generated_mask_img_path)
 
             # Save BOLD mask and link it to the BOLD data type dict;
@@ -686,7 +686,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         # Fix t_r as nilearn messes it up
         cleaned_img.header["pixdim"][4] = t_r
         # Save deconfounded data
-        deconfounded_img_path = element_tempdir / "deconfounded_data.nii.gz"
+        deconfounded_img_path = element_tempdir / "deconfounded_data.nii"
         nib.save(cleaned_img, deconfounded_img_path)
 
         logger.debug("Updating `BOLD`")

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/smoothing/_fsl_smoothing.py

@@ -79,9 +79,10 @@ class FSLSmoothing:
         element_tempdir = WorkDirManager().get_element_tempdir(
             prefix="fsl_susan"
         )
-        susan_out_path = element_tempdir / "smoothed_data.nii.gz"
+        susan_out_path = element_tempdir / "smoothed_data.nii"
         # Set susan command
         susan_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "susan",
             f"{input['path'].resolve()}",
             f"{brightness_threshold}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/smoothing/_nilearn_smoothing.py

@@ -74,7 +74,7 @@ class NilearnSmoothing:
         smoothed_img = nimg.smooth_img(imgs=input["data"], fwhm=fwhm)
 
         # Save smoothed output
-        smoothed_img_path = element_tempdir / "smoothed_data.nii.gz"
+        smoothed_img_path = element_tempdir / "smoothed_data.nii"
         nib.save(smoothed_img, smoothed_img_path)
 
         logger.debug("Updating smoothed data")

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/warping/_ants_warper.py

@@ -16,6 +16,7 @@ from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies, SpaceLike
 from ...utils import raise_error, run_ext_cmd
 from ..base import logger
+from ._utils import warp_in_chunks
 
 
 __all__ = ["ANTsWarper"]
@@ -93,7 +94,7 @@ class ANTsWarper:
 
             # Create a tempfile for resampled reference output
             resample_image_out_path = (
-                element_tempdir / "resampled_reference.nii.gz"
+                element_tempdir / "resampled_reference.nii"
             )
             # Set ResampleImage command
             resample_image_cmd = [
@@ -109,21 +110,27 @@ class ANTsWarper:
             run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
 
             # Create a tempfile for warped output
-            apply_transforms_out_path = element_tempdir / "warped_data.nii.gz"
-            # Set antsApplyTransforms command
-            apply_transforms_cmd = [
-                "antsApplyTransforms",
-                "-d 3",
-                "-e 3",
-                "-n LanczosWindowedSinc",
-                f"-i {input['path'].resolve()}",
-                # use resampled reference
-                f"-r {resample_image_out_path.resolve()}",
-                f"-t {warp_file_path.resolve()}",
-                f"-o {apply_transforms_out_path.resolve()}",
-            ]
-            # Call antsApplyTransforms
-            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+            apply_transforms_out_path = element_tempdir / "warped_data.nii"
+            # Call antsApplyTransforms in single precision, in chunks of
+            # volumes
+            warp_in_chunks(
+                name="antsApplyTransforms",
+                input_path=input["path"].resolve(),
+                output_path=apply_transforms_out_path.resolve(),
+                cmd=lambda in_path, out_path: [
+                    "antsApplyTransforms",
+                    "-d 3",
+                    "-e 3",
+                    "-n LanczosWindowedSinc",
+                    "--float 1",
+                    f"-i {in_path}",
+                    # use resampled reference
+                    f"-r {resample_image_out_path.resolve()}",
+                    f"-t {warp_file_path.resolve()}",
+                    f"-o {out_path}",
+                ],
+                tempdir=element_tempdir,
+            )
 
             logger.debug("Updating warped data")
             input.update(
@@ -145,7 +152,7 @@ class ANTsWarper:
             if input.get("mask") is not None:
                 # Create a tempfile for warped mask output
                 apply_transforms_mask_out_path = (
-                    element_tempdir / "warped_mask.nii.gz"
+                    element_tempdir / "warped_mask.nii"
                 )
                 # Set antsApplyTransforms command
                 apply_transforms_mask_cmd = [
@@ -153,6 +160,7 @@ class ANTsWarper:
                     "-d 3",
                     "-e 3",
                     "-n 'GenericLabel[NearestNeighbor]'",
+                    "--float 1",
                     f"-i {input['mask']['path'].resolve()}",
                     # use resampled reference
                     f"-r {input['reference']['path'].resolve()}",
@@ -212,7 +220,7 @@ class ANTsWarper:
                     # Create a tempfile for resampled reference output
                     ref_path = (
                         element_tempdir
-                        / f"resampled_reference-{reference}.nii.gz"
+                        / f"resampled_reference-{reference}.nii"
                     )
                     # Set ResampleImage command
                     resample_image_cmd = [
@@ -243,27 +251,33 @@ class ANTsWarper:
                     extra_input=None,
                 )
                 # Save template
-                ref_path = element_tempdir / f"{reference}_T1w.nii.gz"
+                ref_path = element_tempdir / f"{reference}_T1w.nii"
                 nib.save(template_space_img, ref_path)
 
             # Create a tempfile for warped output
             warped_output_path = element_tempdir / (
-                f"warped_data_from_{input_space}_to_{reference}.nii.gz"
+                f"warped_data_from_{input_space}_to_{reference}.nii"
             )
 
-            # Set antsApplyTransforms command
-            apply_transforms_cmd = [
-                "antsApplyTransforms",
-                "-d 3",
-                "-e 3",
-                "-n LanczosWindowedSinc",
-                f"-i {input['path'].resolve()}",
-                f"-r {ref_path.resolve()}",
-                f"-t {xfm_file_path.resolve()}",
-                f"-o {warped_output_path.resolve()}",
-            ]
-            # Call antsApplyTransforms
-            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+            # Call antsApplyTransforms in single precision, in chunks of
+            # volumes
+            warp_in_chunks(
+                name="antsApplyTransforms",
+                input_path=input["path"].resolve(),
+                output_path=warped_output_path.resolve(),
+                cmd=lambda in_path, out_path: [
+                    "antsApplyTransforms",
+                    "-d 3",
+                    "-e 3",
+                    "-n LanczosWindowedSinc",
+                    "--float 1",
+                    f"-i {in_path}",
+                    f"-r {ref_path.resolve()}",
+                    f"-t {xfm_file_path.resolve()}",
+                    f"-o {out_path}",
+                ],
+                tempdir=element_tempdir,
+            )
 
             logger.debug("Updating warped data")
             input.update(
@@ -287,7 +301,7 @@ class ANTsWarper:
                 logger.debug("Warping associated mask")
                 # Create a tempfile for warped mask output
                 apply_transforms_mask_out_path = element_tempdir / (
-                    f"warped_mask_from_{input_space}_to_{reference}.nii.gz"
+                    f"warped_mask_from_{input_space}_to_{reference}.nii"
                 )
                 # Set antsApplyTransforms command
                 apply_transforms_mask_cmd = [
@@ -295,6 +309,7 @@ class ANTsWarper:
                     "-d 3",
                     "-e 3",
                     "-n 'GenericLabel[NearestNeighbor]'",
+                    "--float 1",
                     f"-i {input['mask']['path'].resolve()}",
                     # use resampled reference or original
                     f"-r {ref_path.resolve()}",

{junifer-0.0.8.dev329 → junifer-0.0.8.dev335}/junifer/preprocess/warping/_fsl_warper.py

@@ -15,6 +15,7 @@ from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
 from ...utils import raise_error, run_ext_cmd
 from ..base import logger
+from ._utils import warp_in_chunks
 
 
 __all__ = ["FSLWarper"]
@@ -93,9 +94,10 @@ class FSLWarper:
                 )
 
             # Create a tempfile for resampled reference output
-            flirt_out_path = element_tempdir / "resampled_reference.nii.gz"
+            flirt_out_path = element_tempdir / "resampled_reference.nii"
             # Set flirt command
             flirt_cmd = [
+                "FSLOUTPUTTYPE=NIFTI",
                 "flirt",
                 "-interp spline",
                 f"-in {extra_input['T1w']['path'].resolve()}",
@@ -107,19 +109,24 @@ class FSLWarper:
             run_ext_cmd(name="flirt", cmd=flirt_cmd)
 
             # Create a tempfile for warped output
-            applywarp_out_path = element_tempdir / "warped_data.nii.gz"
-            # Set applywarp command
-            applywarp_cmd = [
-                "applywarp",
-                "--interp=spline",
-                f"-i {input['path'].resolve()}",
-                # use resampled reference
-                f"-r {flirt_out_path.resolve()}",
-                f"-w {warp_file_path.resolve()}",
-                f"-o {applywarp_out_path.resolve()}",
-            ]
-            # Call applywarp
-            run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+            applywarp_out_path = element_tempdir / "warped_data.nii"
+            # Call applywarp in chunks of volumes
+            warp_in_chunks(
+                name="applywarp",
+                input_path=input["path"].resolve(),
+                output_path=applywarp_out_path.resolve(),
+                cmd=lambda in_path, out_path: [
+                    "FSLOUTPUTTYPE=NIFTI",
+                    "applywarp",
+                    "--interp=spline",
+                    f"-i {in_path}",
+                    # use resampled reference
+                    f"-r {flirt_out_path.resolve()}",
+                    f"-w {warp_file_path.resolve()}",
+                    f"-o {out_path}",
+                ],
+                tempdir=element_tempdir,
+            )
 
             logger.debug("Updating warped data")
             input.update(
@@ -140,11 +147,10 @@ class FSLWarper:
             # Check for data type's mask and warp if found
             if input.get("mask") is not None:
                 # Create a tempfile for warped mask output
-                applywarp_mask_out_path = (
-                    element_tempdir / "warped_mask.nii.gz"
-                )
+                applywarp_mask_out_path = element_tempdir / "warped_mask.nii"
                 # Set applywarp command
                 applywarp_mask_cmd = [
+                    "FSLOUTPUTTYPE=NIFTI",
                     "applywarp",
                     "--interp=nn",
                     f"-i {input['mask']['path'].resolve()}",
@@ -201,10 +207,11 @@ class FSLWarper:
                 logger.debug("Resampling reference to match input resolution")
                 # Create a tempfile for resampled reference output
                 ref_path = (
-                    element_tempdir / f"resampled_reference-{reference}.nii.gz"
+                    element_tempdir / f"resampled_reference-{reference}.nii"
                 )
                 # Set flirt command
                 flirt_cmd = [
+                    "FSLOUTPUTTYPE=NIFTI",
                     "flirt",
                     "-interp spline",
                     f"-in {input['reference']['path'].resolve()}",
@@ -220,21 +227,25 @@ class FSLWarper:
 
             # Create a tempfile for warped output
             applywarp_out_path = (
-                element_tempdir
-                / f"warped_data_from_native_to_{reference}.nii.gz"
+                element_tempdir / f"warped_data_from_native_to_{reference}.nii"
+            )
+            # Call applywarp in chunks of volumes
+            warp_in_chunks(
+                name="applywarp",
+                input_path=input["path"].resolve(),
+                output_path=applywarp_out_path.resolve(),
+                cmd=lambda in_path, out_path: [
+                    "FSLOUTPUTTYPE=NIFTI",
+                    "applywarp",
+                    "--interp=spline",
+                    f"-i {in_path}",
+                    # use resampled reference or original
+                    f"-r {ref_path.resolve()}",
+                    f"-w {warp_file_path.resolve()}",
+                    f"-o {out_path}",
+                ],
+                tempdir=element_tempdir,
             )
-            # Set applywarp command
-            applywarp_cmd = [
-                "applywarp",
-                "--interp=spline",
-                f"-i {input['path'].resolve()}",
-                # use resampled reference or original
-                f"-r {ref_path.resolve()}",
-                f"-w {warp_file_path.resolve()}",
-                f"-o {applywarp_out_path.resolve()}",
-            ]
-            # Call applywarp
-            run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
 
             logger.debug("Updating warped data")
             input.update(
@@ -258,10 +269,11 @@ class FSLWarper:
                 # Create a tempfile for warped mask output
                 applywarp_mask_out_path = (
                     element_tempdir
-                    / f"warped_mask_from_native_to_{reference}.nii.gz"
+                    / f"warped_mask_from_native_to_{reference}.nii"
                 )
                 # Set applywarp command
                 applywarp_mask_cmd = [
+                    "FSLOUTPUTTYPE=NIFTI",
                     "applywarp",
                     "--interp=nn",
                     f"-i {input['mask']['path'].resolve()}",