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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