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
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
