SKULL STRIPPING USING "HDBrainExtraction"

Support
1

Operating system: windows 11
Slicer version: 5.0.3 r30893/7eaof43
Expected behavior: skull stripping
Actual behavior:

Failed to compute results.

Command '['C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'git+https://github.com/MIC-DKFZ/batchgenerators#egg=batchgenerators']' returned non-zero exit status 1.
Traceback (most recent call last):
  File "C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/HDBrainExtraction/lib/Slicer-5.0/qt-scripted-modules/HDBrainExtractionTool.py", line 227, in onApplyButton
    self.logic.setupPythonRequirements()
  File "C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/HDBrainExtraction/lib/Slicer-5.0/qt-scripted-modules/HDBrainExtractionTool.py", line 301, in setupPythonRequirements
    slicer.util.pip_install('git+https://github.com/MIC-DKFZ/batchgenerators#egg=batchgenerators')
  File "C:\Users\admin\AppData\Local\NA-MIC\Slicer 5.0.3\bin\Python\slicer\util.py", line 3527, in pip_install
    _executePythonModule('pip', args)
  File "C:\Users\admin\AppData\Local\NA-MIC\Slicer 5.0.3\bin\Python\slicer\util.py", line 3490, in _executePythonModule
    logProcessOutput(proc)
  File "C:\Users\admin\AppData\Local\NA-MIC\Slicer 5.0.3\bin\Python\slicer\util.py", line 3459, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'git+https://github.com/MIC-DKFZ/batchgenerators#egg=batchgenerators']' returned non-zero exit status 1.

plz do help me what to do.

2

Could you try to locally edit the file

C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/HDBrainExtraction/lib/Slicer-5.0/qt-scripted-modules/HDBrainExtractionTool.py

by editing line 301 implementing the following change:

-slicer.util.pip_install('git+https://github.com/MIC-DKFZ/batchgenerators#egg=batchgenerators')
+slicer.util.pip_install("batchgenerators")

For reference, here is also link to the corresponding source file. See HDBrainExtractionTool/HDBrainExtractionTool.py#L301

I suspect the problem is due to the fact you may not have git installed.