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