Hi Freesurfer support team,

I'm attempting to register coordinates between BrainVoyager anatomical images and freesurfer segmented images with both in native space, however I'm running into inconsistencies specifically along the inferior/superior dimension that I hope you can help me with

BrainVoyager reports coordinates as voxel indices which I'm trying to match with FreeView's T1fs_nu_conform coordinates which I assume are in voxel indices as well. Both the AP and RL dimensions match in both programs across all our participants, however the SI axis does not, with offsets varying across participants.

Does the recon-all function crop the image such that the Z dimension is no longer matched with native space? I've noticed that the images are cropped specifically from the bottom segment below the neck and was wondering if that was affecting the coordinate report in the SI axis. If this is the case, is this stored in freesurfer such that I can get coordinates relative to the uncropped image or just the offset value for the Z coordinate to compensate for it?

Thanks,

Jerry Jeyachandra