Hi Joe
you can use mri_convert to convert the .mgz volume to nifti if that is what you want:
mri_convert aseg.mgz aseg.nii.gz
should do the trick. Not sure if that counts as an ROI for SPM. If you want separate volumes for each structure I think you can use mri_binarize with the --match flag
cheers Bruce
On Thu, 15 Feb 2018, Simon, Joe wrote:
Dear Experts
I just recently started using Freesurfer (implemented as a virtual machine on a Windows machine). After having completed the recon-all procedure, I now want to export the subcortical segementation as .nii images for further use in SPM. My aim is to have a ROI for each segmented subcortical structure. What would be the easiest way to do this? Any help is appreciated.
Thanks a lot!
Best regards,
Joe
Dr. Dipl.-Psych. Joe Simon
Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik
Im Neuenheimer Feld 410 69120
Tel.: ++49(0)6221-56-38667 joe.simon@med.uni-heidelberg.de