# SKULL STRIPPING USING "HDBrainExtraction"

**URL:** <https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795>\
**Category:** Support\
**Created:** [October 20, 2022, 5:25am UTC](https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795 "2022-10-20T05:25:01Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![D.Prasad](https://avatars.discourse-cdn.com/v4/letter/d/a88e57/32.png) [@D.Prasad](https://discourse.slicer.org/u/D.Prasad)\
**Post date:** [October 20, 2022, 5:25am UTC](https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795/1 "2022-10-20T05:25:01Z")

</div>

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

Failed to compute results.

```auto
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.

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [October 20, 2022, 6:16am UTC](https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795/2 "2022-10-20T06:16:05Z")

</div>

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:

```diff
-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](https://github.com/lassoan/SlicerHDBrainExtraction/blob/c308995da9ded06c0833f8c3681e8202005db99d/HDBrainExtractionTool/HDBrainExtractionTool.py#L301)

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