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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 <operl...@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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