About SwissSkullStripper

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.

Crtl + 4 open 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.


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

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


It seems that you have not loaded the mask image as a labelmap. I’ve updated Swiss skull stripper module documentation to make this step more clear. Please follow the steps described there and let us know if you have any problems.

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.

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.

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

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