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Hi again,

mri_convert will give you the voxel size, which is isotropic. Multiply 2 of the dimensions and you’ve got the area.

Also: rather than counting pixels from the discrete segmentation, I highly recommend that you produce soft segmentations as explained in my previous email. Then, you can weigh the area of each pixel in each slice by it’s probability.

Cheers,

/Eugenio

 

-- 

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 11:28
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: 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:

MailScanner has detected a possible fraud attempt from "eur01.safelinks.protection.outlook.com" claiming to be 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)

MailScanner has detected a possible fraud attempt from "eur01.safelinks.protection.outlook.com" claiming to be 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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