5ttgen [ERROR] unknown option "-premasked" on HCP tutorial


I’m trying to follow the HCP tutorial (http://mrtrix.readthedocs.io/en/latest/tutorials/hcp_connectome.html)
but when I run the first 5tt command I get the following error:

5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked
5ttgen: [ERROR] unknown option “-premasked”

Can you give me instructions about how to go on with the tutorial?



Hi Danilo,

The most likely explanation is that your version of MRtrix3 is out-of-date. The -premasked option was added along the way at some point; so while it’s available in the newest code, and the online documentation shows it as available (and even demonstrates its use in that tutorial), your local installation of MRtrix3 doesn’t have it. So using git pull to download the most recent code should make the option available. (Don’t forget to ./build the commands after the download!)