Editing mask after Swiss Skull Stripping

Hi, I have used the Swiss Skull Stripper module to create a mask of a brain from an MRI. However, the mask that was generated includes some of the eye. Is there a way I can remove this from my mask? I have tried using the segment editor but it says there are no segments, so I can’t erase anything.

To allow editing of a labelmap volume in Segment Editor module, you first need to convert it to a segmentation. You can do that by right-clicking on it in Data module and choosing “Convert labelmap to segmentation node”.

You can use “Mask volume” effect in Segment Editor to apply the modified mask to the MRI image. “Mask volume” effect is available after you install “SegmentEditorExtraEffects” extension.

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I have converted the mask to a labelmap and edited it. I wanted to save the binary mask to use Pyradiomics. I did this by right clicking the patient mask label in the ‘data’ module, and selecting ‘export visible segments to binary map’. However, when I try to run this with Pyradiomics, it does not work (it works when I run it with the original mask created using swiss skull stripper, but does not run with the edited mask). Is there another way I am supposed to save this new mask?

Could you try to use the export/import section in Segmentations module and choose the original mask as reference volume? If it still fails then please tell us what error pyradiomics reported.

I ended up clicking the 2 boxes on the right hand side of ‘master volume’ in the segment editor. I think the geometries were slightly different. It all works now. Thanks for all your help :slight_smile:

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