Matt,

mri_extract_label can be used to extract one or more regions.

for example:

mri_extract_label aparc+aseg.mgz 17 53 hippo.nii.gz

will extract left and right hippocampus, creating the file hippo.nii.gz.

refer to the file $FREESURFER_HOME/FreeSurferColorLUT.txt for label numbers.

Nick

On Wed, 2008-03-12 at 15:59 -0400, Doug Greve wrote:

you can use mri_convert, eg

mri_convert aparc+aseg.mgz aparc+aseg.nii

Matthew A. Garlinghouse wrote:

...

Hi,

New to Freesurfer. Is it possible to export specific cortical regions/surfaces from the annotations file in a .nii or analyze image format?

Best,

Matt _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer