New extension

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Nov 14 '24 12:11 ErenArkun

This will be great, thank you for your contribution!

I've tried to use your module but it failed to load, with this error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\andra\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-01\lib\Python\Lib\imp.py", line 169, in load_source
    module = _exec(spec, sys.modules[name])
  File "<frozen importlib._bootstrap>", line 613, in _exec
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "C:/D/SlicerBrainParcellation275/slicer-brain-parcellation275/BrainSegmentation.py", line 3, in <module>
    import nibabel as nib
ModuleNotFoundError: No module named 'nibabel'
[Qt] loadSourceAsModule - Failed to load file "C:/D/SlicerBrainParcellation275/slicer-brain-parcellation275/BrainSegmentation.py"  as module "BrainSegmentation" !
[Qt] Fail to instantiate module  "BrainSegmentation"
[Python] The module factory manager reported an error. One or more of the requested module(s) and/or dependencies thereof may not have been loaded.

The issue is that in the module .py file (BrainSegmentation.py) you can only import Python modules at the file level that are built-in Python modules or they are in packages that are bundled with Slicer. In your Slicer module you can install any packages that you need later, and then import them inside functions or in Python modules (for example, in your utils subfolder).

Specifically, these imports needs to go:

import nibabel as nib
from nibabel import processing
import torch
from tqdm import tqdm as std_tqdm

Since many extensions use pytorch, it is a huge package, and its installation is not trivial, it has to be installed via the SlicerPytorch extension. See a complete example here: https://github.com/lassoan/SlicerTotalSegmentator/blob/c4144875e600705f4c4b30a44b49d05d27ffb757/TotalSegmentator/TotalSegmentator.py#L757-L776

A few more small comments:

Remove temporary __pycache__ folders from the git repository
Some of the files in https://github.com/ErenArkun/SlicerBrainParcellation275/tree/main/slicer-brain-parcellation275/level folder might be redundant. You may be able to store complex data structures in a .json file that you can load into Python by a single command and then you don't .

Nov 16 '24 03:11 lassoan

Thank you for your feedback. I will look into the issue you encountered.

Nov 26 '24 18:11 ErenArkun

Let us know if you have completed your revisions and your extension is ready for review.

Dec 02 '24 21:12 lassoan

Some automatic validation checks failed. They need to be fixed before the extension can be added to the Extensions Index.

Sep 07 '25 02:09 lassoan

Add SlicerBrainParcellation275 extension

New extension