Re: [Freesurfer] recon-all transformations: raw nii to T1.mgz
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 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 *On Behalf Of *Peled, Noam *Sent:* Tuesday, April 6, 2021 2:52 PM *To:* freesurfer@nmr.mgh.harvard.edu *Cc:* Perlman, Or *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: 1.78, 1.78, 1.78 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all transformations: raw nii to T1.mgz
Hi Noam You can always use the -rl 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 On Behalf Of Peled, Noam Sent: Tuesday, April 6, 2021 2:52 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Perlman, Or 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: 1.78, 1.78, 1.78 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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: 1.78, 1.78, 1.78 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
