# About SwissSkullStripper

**URL:** <https://discourse.slicer.org/t/about-swissskullstripper/7544>\
**Category:** Support\
**Created:** [July 12, 2019, 2:26am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544 "2019-07-12T02:26:34Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![otanit](https://avatars.discourse-cdn.com/v4/letter/o/ea666f/32.png) [@otanit](https://discourse.slicer.org/u/otanit)\
**Post date:** [July 12, 2019, 2:26am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/1 "2019-07-12T02:26:34Z")

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Operating system: Windows 10  
Slicer version: Slicer 4.10.1  
Expected behavior: Install SwissSkullStripper and calculate intracranial content volume with it.  
Actual behavior: Cannot install SwissSkullStripper and use the necessary modules in it.

I’m trying to calculate intracranial content volumes using SwissSkullStripper. However, I don’t know how to install it.  
I appreciate any advice and Information on its installation and usage.  
Thanks a lot.

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**Author:** ![cyufu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cyufu/32/1779_2.png) [@cyufu](https://discourse.slicer.org/u/cyufu)\
**Post date:** [July 12, 2019, 5:03am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/2 "2019-07-12T05:03:11Z")

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Crtl + 4 open Extensions Manager

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/2/e2dcca82df07f7f3966806c19dfeced193c2e29d.png)

More

[https://www.slicer.org/wiki/Documentation/4.10/Modules/SwissSkullStripper](https://www.slicer.org/wiki/Documentation/4.10/Modules/SwissSkullStripper)

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**Author:** ![otanit](https://avatars.discourse-cdn.com/v4/letter/o/ea666f/32.png) [@otanit](https://discourse.slicer.org/u/otanit)\
**Post date:** [July 14, 2019, 10:21am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/3 "2019-07-14T10:21:34Z")

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> [@cyufu](#):
>
> Extensions Manager

Thank you very much for your kind advice.  
Could you please inform me how can I go to the Extensions Manager web site?  
I tried to find it but I couldn’t.

I am trying to use 3D slicer and Skull Stripper on the windows OS (not Linux).  
I appreciate your kind information and advice.

Best,

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 14, 2019, 1:42pm UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/4 "2019-07-14T13:42:58Z")

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> [@otanit](#):
>
> Could you please inform me how can I go to the Extensions Manager web site?

You don’t need to open the website manually, but use the extension manager from Slicer as @cyufu

If for some reason you were interested in how to access the extension manager from outside Slicer, you can find instructions here: [Documentation/Nightly/SlicerApplication/ExtensionsManager - Slicer Wiki](https://www.slicer.org/wiki/Documentation/Nightly/SlicerApplication/ExtensionsManager)

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**Author:** ![otanit](https://avatars.discourse-cdn.com/v4/letter/o/ea666f/32.png) [@otanit](https://discourse.slicer.org/u/otanit)\
**Post date:** [July 14, 2019, 10:33pm UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/5 "2019-07-14T22:33:35Z")

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Following your kind information, I could download SwissSullStripper and add it to 3D Slicer.  
Then, I input all the necessary files in the SwissSkullStripper module following the instruction of SwissSkullStripper (please see the attached photo).  
In this process, I could not select Atlas Mask Volume at first.  
Therefore, I chose Rename current LabelMapVolume and rename it as “atlasMask”, and click “Apply”.  
However, the following error message appeared after that.  
What should I do to address this problem?  
I appreciate your kind instruction and advice.

ERROR MESSAGE shown in the SwissSkullStripper module.

* * *

Failed to read input atlas label volume.  
itk::ExceptionObject (00000028C6DDA100)  
Location: “unknown”  
File: D:\D\S\Slicer-4101-build\ITK\Modules\IO\ImageBase\src\itkImageIOBase.cxx  
Line: 378  
Description: itk::ERROR: MRMLIDImageIO(00000028CB555940): Unknown component type: 0

* * *

H

 ![Question%20photo%20about%20SwissSkullStripper](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/e/9e28fc9af170df076793970570a410d4c96795a5.jpeg)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 16, 2019, 1:01pm UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/6 "2019-07-16T13:01:15Z")

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It seems that you have not loaded the mask image as a labelmap. I’ve updated [Swiss skull stripper module documentation](https://www.slicer.org/wiki/Documentation/Nightly/Modules/SwissSkullStripper) to make this step more clear. Please follow the steps described there and let us know if you have any problems.

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**Author:** ![otanit](https://avatars.discourse-cdn.com/v4/letter/o/ea666f/32.png) [@otanit](https://discourse.slicer.org/u/otanit)\
**Post date:** [July 22, 2019, 10:34pm UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/7 "2019-07-22T22:34:48Z")

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Thank you for your kind advice.  
Following your advice and module documentation, I could use mask image as a labelmap and create Patient Mask Label by SwissSkullStripper.

I have another consultation here.  
I need to calculate intracranial content volume.

1. To my understanding, the Patient Mask Label volume is the same as intracranial content volume.
2. Since the Mask Label is not segmented, I have to use Label Statistics in order to calculate Patient Mask Label volume (intracranial content volume) in this case.  
Is my understanding above correct?  
I would like to receive your advice, if I have some misunderstanding or there is other necessary steps for calculating intracranial volume.  
I appreciate your kind advice.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 23, 2019, 6:46pm UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/8 "2019-07-23T18:46:38Z")

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The steps are correct, you can compute the intracranial volume like that.

For more metrics, you can convert “Patient Mask Label volume” to segmentation in Data module (right-click on the label volume and choose to convert to segmentation) and use Segment Statistics module.

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<div class="post-metadata">

**Author:** ![otanit](https://avatars.discourse-cdn.com/v4/letter/o/ea666f/32.png) [@otanit](https://discourse.slicer.org/u/otanit)\
**Post date:** [July 24, 2019, 1:09am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544/9 "2019-07-24T01:09:13Z")

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I greatly appreciate your kind advice.  
I could calculate ICC volume with your and Dr. cyufu’s instruction.  
Thanks a lot.