Rodent skull stripping

I am interested in performing skull stripping and bias corrections for rodent data from a Bruker scanner. Since I have become comfortable with Slicer and working with DTI data in it, I was hoping that there might be some good tools in Slicer for these two additional steps. As well as a good how to guide.

Any suggestions would be appreciated.


SwissSkullStripper extension should work well for rodent skulls. You just need to provide a pair of rodent MRI and corresponding labelmap that contains only the brain in Atlas section of the module. You can create a brain labelmap by manually segmenting the brain using Segment editor module and then exporting the segment to a labelmap. Let us know if it worked.

You can perform bias correction using “N4ITK MRI Bias correction” module.

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4 posts were split to a new topic: Canine skull stripping