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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, /E
-- 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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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