Hi Jessica

in general if you specify .nii or .nii.gz as the extension of any output file we will write it in nifti format. This makes using mri_convert easy:

mri_convert any_volume.mgz any_volume.nii.gz

should work fine cheers Bruce

On Sun, 31 May 2020, Hua, Jessica wrote:

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Hi FreeSurfer experts,

Also in case the code is different, how would I convert my T1.mgz  file to a .nii file to be used in DTI analyses?

Thanks!

Jessica

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Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology  University of Missouri