Hi Bruce

Thanks, mri_binarize works great!

Best, 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 ---------------------------------------------------------------- Date: Thu, 15 Feb 2018 12:08:12 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1802151207140.11691@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"

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