Re: [Freesurfer] Pixel values in Brainstem segmentation

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Hi, Eugenia

I need the real area size of the brainstem in one slice, I can calculate the total pixels in the area from *brainstemSsLabels.v10.mgz*, I need the real pixel size of it, than I can calculate the real area size. Many Thanks!

Best Jackie

On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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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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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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