Hi Prasanna,

not sure what you are asking and what this has to do with longitudinal. But generally: subcortical segmentations are stored in the aseg.mgz file (this is true also for the longituinal stream, do not look at the aseg.fused.mgz , it is an intermediate step). Final results are in aseg.mgz.

Aparc is for the parcellations of the cortex.

Freesurfer has tools to create e.g. a hippocampus mask from the aseg. mri_pretess can probably do it and cleans up the mask a little.

Best, Martin

On Fri, 2012-12-07 at 11:04 -0700, Prasanna M wrote:

Hi,

Do I work with aseg.fused.mgz or do I work with aparc files to get the most accurate segmentation of brain structures?

I tried using freeview to look at segmentations. Is there a way to isolate mgz files of very specific structures. I mean, is there an inbuilt tool which can do that for me, or would I have to go image by image, and threshold to get, say the hippocampus?

Thanks, Prasanna

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