Dear Jackie,

You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see:

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

Also: you can obtain the voxel size with:

mri_info brainstemSsLabels.v10.mgz

Cheers,

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Min Zhang <jacqueline.m.zhang@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 16 July 2019 at 09:58
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation

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To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. I used the result in brainstemSsLabels.v10.mgz. Many Thanks!

Best

Jackie