Tractseg: DeprecationWarning: pkg_resources is deprecated as an API.

[Ramtilakgattu]

Hello all,

I installed TractSeg on virtualbox Linux Ubuntu (that was downloaded as a part of Freesurfer VB installation). I am trying to test the installation by running TractSeg -i Diffusion.nii.gz --raw_diffusion_input but it doesnt run at all. Here is the message that I receive on the terminal.

"**TractSeg -i Diffusion.nii.gz --raw_diffusion_input
/home/developer/anaconda3/bin/TractSeg:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').require('TractSeg==2.9')
Creating brain mask...
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
Creating peaks (1 of 3)...
Traceback (most recent call last):
File "/home/developer/anaconda3/bin/dwi2response", line 127, in
import mrtrix3
File "/home/developer/anaconda3/bin/mrtrix3.py", line 17, in
import imp, os, sys
ModuleNotFoundError: No module named 'imp'
Creating peaks (2 of 3)...
dwi2fod: [ERROR] Unable to open numerical data text file "tractseg_output/response.txt": No such file or directory
dwi2fod: [ERROR] CSD algorithm expects second argument to be the input response function file
Creating peaks (3 of 3)...
sh2peaks: [ERROR] cannot access file "tractseg_output/WM_FODs.nii.gz": No such file or directory
sh2peaks: [ERROR] error opening image "tractseg_output/WM_FODs.nii.gz"
Traceback (most recent call last):
File "/home/developer/anaconda3/lib/python3.12/site-packages/nibabel/loadsave.py", line 101, in load
stat_result = os.stat(filename)
^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'tractseg_output/peaks.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/developer/anaconda3/bin/TractSeg", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/developer/TractSeg/bin/TractSeg", line 420, in
main()
File "/home/developer/TractSeg/bin/TractSeg", line 258, in main
data_img = nib.load(peak_path)
^^^^^^^^^^^^^^^^^^^
File "/home/developer/anaconda3/lib/python3.12/site-packages/nibabel/loadsave.py", line 103, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'tractseg_output/peaks.nii.gz'**

Can someone help me in resolving the issue,

I tried installing with -e option but that didnt solve the problem.

Thanks

Regards
Tilak

[antonpst]

HI, @Ramtilakgattu!

I do not think the title of this issue

Tractseg: DeprecationWarning: pkg_resources is deprecated as an API.

matches your question well. However, addressing the header of your issue:

(0)

To get rid of the "DeprecationWarning" w.r.t. pkg_resourcesmodule of setuptools you could simply fall back to the latest version of setuptools which does not have the warning, i.e.

pip uninstall setuptools
pip install setuptools==66.1.1

v67.3. ships the warning for the first time, see here and here. As mentioned in the comments, this is "the equivalent of destroying the check engine light once it lights up.". It's obviously bad. Do not do this; ignore the warning message for now.

% TractSeg -i Diffusion.nii.gz --raw_diffusion_input fails:

(1)

ModuleNotFoundError: No module named 'imp'

Which python version are you sitting on? >v3.11? You can either fall back to v3.11 or add

from importlib import import_module

to TractSeg I suspect. Related SO q.

(2)

FileNotFoundError: [Errno 2] No such file or directory: 'tractseg_output/peaks.nii.gz'

After a failed attempt, make sure to delete tractseg_output directory and its potentially faulty contents. This makes life easier.

When running TractSeg -i Diffusion.nii.gz --raw_diffusion_input from a terminal, you should execute the command from inside the directory where the (example) file Diffusion.nii.gz (and .bvals and bevels) lies. Otherwise you need to specify paths.