I am trying to improve the mask for participants with lesions. I wanted to try running dwi2mask synthstrip on the dwi image since this worked well in FreeSurfer with the T1. However, I get the following error:
dwi2mask has nothing to do with synthstrip (see dwi2mask — MRtrix3 3.0 documentation). dwi2mask only expects an input and output. Any options are preceded with “-”
Synthtrip is part of freesurfer as mri_synthstrip or can be installed as, for example, a singularity container from SynthStrip
In the developers branch, there is a new dwi2mask command that allows you to use different algorithms. One of them is synthstrip. To use that you need to install the developers branch, as (I think) this has not been yet officially merged. I hope this helps.
Thanks very much for your reply. I tried downloading the dev branch but there are no compile or build scripts made when I follow these steps for the dev branch.