Hello Freesurfer team,
I have the unfortunate task of performing longitudinal volumetric analysis on subjects collected on three different scanners with different voxel numbers/sizes. I didn't find this out until attempting to run the longitudinal base and receiving this message:
WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.
By re-registering the original nifti and recreating the norm.mgz/talairach I can correct the geometry, but FSL's Flirt will only work with niftis and not mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes properly. I was wondering if there were any freesurfer tools I could use to simply re-register the .mgz volumes to the new norm.mgz? If so, how would I go about doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, is this something I should even be concerned about?
Thanks, KZ