See whether this helps. You will have to go in the opposite direction, but the idea is the same https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 11/12/2018 02:00 PM, Min Zhang wrote:

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Dear Freesufer team:

I have marked bounding box in the original DICOM File, and applied autorecon1 to do the skull striping for the images. I want to transfer the bounding box to the skull stripped output. How can I get the coordinates transformation matrix between the input and skull stripped output. Many Thanks!

Best Min

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