Segmentation fault after loading weights

[adelesavalle]

Hello,
I have troubles using TractSeg, I get the same error "segmentation fault", using raw diffusion data or directly ODF peaks. I am on OSX, installed tracts with pip, the packages are up to date, I reinstalled the used retrained weights just in case it was what is causing the problem (pretrained_weights_tract_segmentation_v3.npz)
Here is what I usually obtain :

(base) asavalle@MAC-03240202 Images % tractseg -i peaks.nii.gz -o tractseg_output --output_type tract_segmentation --no_postprocess --verbose

/Users/asavalle/Dev/miniconda3/bin/tractseg:13: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Reorienting data...
Loading weights from: /Users/asavalle/.tractseg/pretrained_weights_tract_segmentation_v3.npz
Loading weights ... (/Users/asavalle/.tractseg/pretrained_weights_tract_segmentation_v3.npz)
zsh: segmentation fault tractseg -i peaks.nii.gz -o tractseg_output --output_type tract_segmentation

I saw the 2 issues #241 (comment) and #269 but it does not seem to be the same issues.
What could I do please ?

[giovannividetta]

Hello, @adelesavalle!

It is a common issue related to the MacOs system, which probably does not give access to specific system components (if I remember it was storage memory or something similar).
If you can, try to install and launch TracSeg on an Ubuntu machine. In #269 I reported computer features and dependencies to build the Python environment.

I hope it will be useful!

[antonpst]

Hi, @adelesavalle!

Are you running an Apple Silicon (M-chip/arm64) device or are you sitting on an Intel chip?

Looks like you are running TractSeg via macOS Terminal (bash/zsh). Try running

export OMP_NUM_THREADS=1 
tractseg -i peaks.nii.gz -o tractseg_output --output_type tract_segmentation --no_postprocess --verbose

this disables multi-threading.

When executing (without setting OMP_NUM_THREADS to 1)

TractSeg -i Diffusion.nii.gz --raw_diffusion_input

on

• Mac M4 (macOS 15.4),
• with latest stable versions of dependent packages/libraries (except require [to avoid a warning]),

I am encountering a potentially similar segmentation fault (SIGSEGV) error which is hard to track down. It is always the 3rd thread (default might be 4 threads) which crashes (related #269).

The error is related to OpenMP, PyTorch and numpy I suspect. Currently, I try to understand the call stack around
libomp.dylib and libtorch_cpu.dylib.

Obviously, disabling multi-threading is unsatisfactory. Hopefully, authors or contributors of/to TractSeg will have a deeper look one day. If it's not due to a set-up issue in TractSeg, chances are we can forward the issue to PyTorch (or Numpy).

If considered helpful I will add full crash report and session info.