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

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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

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