Hi Ting

that means $FREESURFER_HOME/bin is not in your path and you need to add it
(and make sure that the environment variable FREESURFER_HOME is set
properly). If it is, you can do:

source $FREESURFER_HOME/SetUpFreeSurfer.csh

Are you new to Linux also?  If so, you might want to go through some basic
tutorials.

cheers
Bruce

On Fri, 19 Jan 2018, Ting Li wrote:

Hi Freesurfer Expert,

I am very new to Freesurfer and have a very basic question. How to convert .nii files to nii.gz? I have tried the mri_convert subject_name.nii to subject_name.nii.gz directly. It gives me an error information that mri_convert: command not found. Thanks for your help!

Best,
Ting



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