Hi Catherine, Does the individual have good surfaces? If so, then it would be better to map the sig.mgh into the individual using the surface transform, something like (run with --help for more info): mri_surf2surf --srcval sig.mgh --srcsubject fsaverage --hemi lh --trgsubject yoursubject --trgval lh.yoursubject.sig.mgh

Then use mri_surf2vol, something like mri_surf2vol --surfval lh.yoursubject.sig.mgh --hemi lh --fillribbon --identity yoursubject --o sig.volume.mgh

doug

Catherine Wan wrote:

Dear Freesurfer-list,

Please excuse me if this question sounds very simple. I work with lesion brains and I want to overlay the group level result (sig.mgh) onto individual brains to check whether it covers the lesion (which we don't want). I first used mri_surf2vol to convert sig.mgh to a volume. I then mri_vol2vol to normalize the individual T1.mgz to the fsaverage T1, but when I overlaid the sig.mgz onto the normalized T1, it didn't look well-registered (see attached jpeg). However, when I overlaid the same sig.mgh onto the fsaverage T1, it looked completely fine. I'm wondering if anyone could tell me how to better register the individual T1 so I can check whether the individual lesion overlaps with the group level results? Some of the brains went through tkregister2 and the segmentation looked fine afterwards.

Any guidance would be much appreciated!

Regards, Catherine

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