On 6 May 2020, at 19:56, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Are you trying to compute the mean at each voxel?
Try
mri_concat file.mgz --mean --o file.mean.mgz
Assuming that file.mgz has multiple frames. If you have each input in a separate file, you can just
mri_concat file1.mgz file2.mgz ... --mean mean.mgz
To compute the stddev, use --std instead of --mean

On 5/6/2020 1:22 PM, Knut J Bjuland wrote:

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Dear Freesurfer experts, 

 
 

I have tried to use mris_calc to calculate mean and std and export the variable to bash with this command, 

mean=$(mris_calc mghfile std), but the array is not stored in mean. Is there any other way to calculate, mean and use it in a bash script apart from using matlab?  

 
 

Best regards 

 
 

Knut Jørgen Bjuland   

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