NIfTI (.nii.gz) loading failure for TotalSegmentator samples in 3D Slicer 5.10.0 on Apple M4 Pro

Support
1

Description:

I am encountering a consistent error when loading multiple samples from the TotalSegmentator dataset in 3D Slicer (version 5.10.0) on an Apple M4 Pro machine.

Environment:

  • 3D Slicer version: 5.10.0
  • OS: macOS (Apple Silicon M4 Pro)
  • Dataset: TotalSegmentator v201
  • File format: .nii.gz (NIfTI compressed)

Issue:

When attempting to load CT volumes (e.g. s0000/ct.nii.gz), 3D Slicer fails to load the file. This issue is not consistent across the dataset, as other samples load correctly.

Error message:

Error occurred while loading the selected files.
Click 'Show details' button and check the application log for more information.
Error: Loading /Users/<user>/Documents/Datasets/Totalsegmentator_dataset_v201/s0000/ct.nii.gz - load failed.

Behavior:

  • The same error occurs across multiple samples, not limited to s0000
  • No additional information is shown in the UI beyond the generic load failure
  • File paths and dataset structure are correct

Expected behavior:

The .nii.gz CT volumes should load normally into Slicer as volumetric data.

Request:

Any insights into:

  • Potential incompatibility with Apple Silicon (M4 Pro) builds
  • Known issues with .nii.gz loading in Slicer 5.10.0
  • Required configuration, plugins, or ITK settings
  • Possible workaround or diagnostic steps
2

I have only managed to succesfully import volumes as NIFTI or NRRD if they are ‘uncompressed’ and saved as a ‘float’ file via the CAST SCALAR VOLUME module. This goes for StradView and Avizo too. If the file is compressed, it usually doesn’t import the full image sequence/volume…

3

Hi Khorlint,

This is a known issue tied to the ITK NIfTI streaming reader crashing during block decompression of heavily compressed .nii.gz files on Apple Silicon (M4/M3 architectures) in Slicer 5.10. Try using python force loader, bypassing the UI reader.as slicers default loader uses general reader.