Hi Doug,

I would like to inquire about the command “ mri_binarize”. In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz …. etc without the need to convert the output “mgz” files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:

mri_binarize --i aseg.mgz  --o precentral.nii --match 1024

The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output “mgz” then convert it to nifti!!

Is this real or I am missing something? Thanks for any advice!

By the way I see this issue came up recently and in both freesurfer V 5.3 and V6

Best,

Mohamad