If it is just visualization, you should be able to just load them in Freeview (assuming that  they share the RAS system)

On 4/6/2021 3:01 PM, Fischl, Bruce wrote:

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

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