My apologies as I misstated some of the data in my first email,

The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one with 0.9mm). Whereas the FOV is different between the scans being 256x256x176 on one acquisition, 224x256x176 on the second and 240x240x180 on the third.

KZ

On Tue, 5 Jul 2016, zalewk@u.washington.edu wrote:

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