External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu> on behalf of Min Zhang <jacqueline.m.zh...@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 External Email - Use Caution 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
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