Hi, experts. We need to use FreeSurfer to process some analyze image data. More specifically, we want to extract the hippocampus surfaces. We know that FreeSurfer has done subcortical segmentation during -autorecon2 stage in recon-all. We have checked the resulting aseg.mgz file and found that it contains all substructures. So we wonder if there is a way to get the separated .mgz files for each substructure or could FreeSurfer generate the subcortical surfaces? Thanks a lot.
Best, Jie
You can extract a binary mask for any structure with mri_binarize --i aseg.mgz --match XX --o yourmask.mgh where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, 17 = left hippo) It is possible to generate hippo surfaces, but we cannot guarantee accuracy. Let me know if you want to know how. doug
Jie Shi wrote:
Hi, experts. We need to use FreeSurfer to process some analyze image data. More specifically, we want to extract the hippocampus surfaces. We know that FreeSurfer has done subcortical segmentation during -autorecon2 stage in recon-all. We have checked the resulting aseg.mgz file and found that it contains all substructures. So we wonder if there is a way to get the separated .mgz files for each substructure or could FreeSurfer generate the subcortical surfaces? Thanks a lot.
Best, Jie
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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Jie Shi