SlicerBrainParcellation275.json

[ErenArkun]

New extension

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  • Extension name
  • Short description: 1-2 sentences, which summarizes what the extension is usable for
  • At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
  • Description of contained modules: at one sentence for each module
  • Tutorial: step-by-step description of at least the most typical use case, include a few screenshots, provide download links to sample input data set
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  • Content of submitted json file is consistent with the top-level CMakeLists.txt file in the repository (dependencies, etc. are the same)
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[lassoan]

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 .

[ErenArkun]

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

[lassoan]

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