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Issue with pydicom_seg while running TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb in Colab #1901

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ajthomas1949 opened this issue Dec 16, 2024 · 0 comments

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@ajthomas1949
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Describe the bug
I have been trying to run TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
on Colab, but get the following error:

ModuleNotFoundError Traceback (most recent call last)

in <cell line: 12>()
10 # Include pydicom_seg for DICOM SEG objects
11 import pydicom
---> 12 import pydicom_seg
13
14 # for downloading data from TCIA

/usr/local/lib/python3.10/dist-packages/pydicom_seg/reader.py in
7 import pydicom
8 import SimpleITK as sitk
----> 9 from pydicom._storage_sopclass_uids import SegmentationStorage
10
11 from pydicom_seg import reader_utils

ModuleNotFoundError: No module named 'pydicom._storage_sopclass_uids'

I tried inserting !pip install --upgrade --no-deps pydicom pydicom_seg
before the import of pydicom but still get the error:

Requirement already satisfied: pydicom in /usr/local/lib/python3.10/dist-packages (3.0.1)
Requirement already satisfied: pydicom_seg in /usr/local/lib/python3.10/dist-packages (0.4.1)


ModuleNotFoundError Traceback (most recent call last)

in <cell line: 13>()
11 get_ipython().system('pip install --upgrade --no-deps pydicom pydicom_seg')
12 import pydicom
---> 13 import pydicom_seg
14
15 # for downloading data from TCIA

/usr/local/lib/python3.10/dist-packages/pydicom_seg/reader.py in
7 import pydicom
8 import SimpleITK as sitk
----> 9 from pydicom._storage_sopclass_uids import SegmentationStorage
10
11 from pydicom_seg import reader_utils

ModuleNotFoundError: No module named 'pydicom._storage_sopclass_uids'

I assume this means that pydicom_seg is somehow corrupted. I'd much appreciate
any guidance you can give. Thanks for providing this valuablee tutorial!

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