Dear MRTrix experts,
I’m using MRtrix 3.0.3 to create a connectome through a scripts that loops through a large number of participants. To be able to go through the QC more sufficient, I was wondering if it is possible to automatically save an image created by mrview. If this is a possibility, what would this command line be?
It would be very useful to include the mrview command and a command that would rewrite the mrview generated image to a file.
As this questions was initially posted on GitHub and reposted in this forum so all users can see it. I’ll add the responses from Ben Jeurissen and Robert Smith to this post:
Yes, this is possible through the combination of the
-capture.* options and the
-exit option from the
mrview command, e.g.
mrview <options to load images and set things up> -capture.folder <output folder> -capture.prefix <output prefix> -capture.grab -exit
mrview -help for more details.
The catch here is that not every single interactive control in
mrview has a corresponding command-line option. Ideally we would change the implementation so that this is always the case (#1438). But if there are isolated functionalities that you need for a specific project, we can potentially provide assistance regarding how to implement just those.