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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.
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?
Thank you!
-Andy