On 6/24/2024 6:47 PM, Andrew Jahn wrote:

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Hello,

I have a raw anatomical image called raw.mgz, which I have manually annotated using Freeview; the resulting annotations are saved in a file called seg.mgz. I want to compare this to the annotations automatically generated by recon-all, so I ran the image through the recon-all processing stream. However, the original dimensions of the raw.mgz image are 256x209x256, and recon-all resamples the image to 256x256x256 resolution.

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

If I want to compare the amount of overlap between my annotations and those generated by FreeSurfer - specifically, the aparc+aseg.mgz file created by recon-all - what is the best way to register the seg.mgz file to aparc+aseg.mgz? I looked through the documentation of mri_vol2vol, but I wasn't sure which registration file to use. Is it one of the transformation files contained in the "transforms" folder from the image that has been processed through recon-all?

use the mri_label2vol command on that page

Thank you!

-Andy

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