Hi Noam

You can always use the -rl <template vol> switch in mri_convert (rl == “reslice like”). So for example

mri_convert -rl rawavg.mgz orig.mgz orig_back_to_raw.mgz

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam
Sent: Tuesday, April 6, 2021 2:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Perlman, Or <OPERLMAN@mgh.harvard.edu>
Subject: [Freesurfer] recon-all transformations: raw nii to T1.mgz

Hello,

I was running recon-all on a raw T1 image with the following properties:

dimensions: 126 x 144 x 88

voxel sizes: 1.777778, 1.777778, 1.780000

Orientation: PSL

Besides the raw T1, I have other nii files with the same dimensions and orientation that I want to visualize on top of the recon-all output T1.mgz.

How can I run the same transformations (and reslicing) that were used in recon-all (from my raw nii file to T1.mgz) on the other nii files?

Thanks!

Noam