About SwissSkullStripper

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1

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.

2

Crtl + 4 open Extensions Manager

image

More

https://www.slicer.org/wiki/Documentation/4.10/Modules/SwissSkullStripper

3

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,

4

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

5

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
Question%20photo%20about%20SwissSkullStripper5504×3096 3.47 MB

6

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.

7

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.
8

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.

9

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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