You can try running mri_coreg, eg, mri_coreg --mov your-non-image.nii.gz --s subject --reg reg.lta The apply it mri_vol2vol --mov your-non-image.nii.gz --lta reg.lta --o you-non-image-in-fs-space.nii.gz

On 3/4/2025 5:59 PM, Chavez, Caitlyn wrote:

External Email - Use Caution

Hello FreeSurfer Community,

I am looking for any help/information/documentation in replicating the transforms performed in FreeSurfer recon_all on a non-mri volume image. I am trying to align the voxel space of a non-mri image with the masking (aseg, seg, parc) outputs of the registered (recon_all) mri_image.

I am sure it is not as simple as running the non-mri image through FreeSurfer recon_all, but I am unsure how to align the images with the exact same parameters previously used. If there is a method of extracting the parameters and the algorithm from FreeSurfer to register the non-mri images using python I would also be interested in learning about this as well.

Any help/information/documentation is greatly appreciated.  Thank you in advance for your help!

Best,

Caitlyn

Additional information: recon-all -i subject_1.nii.gz -subjid subject_1 -all  ##(Successful run from the command line ) Program versions used: 7.2.0 (freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b) 7.2.0

Non-mri image info Can be converted to .npy or .nii format

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer