Extract current view settings in mrview GUI as a json or dict

1

Hello,

I want to apply all the settings that I applied on a given image to several other images using a python script. In other words, I am lazy, and I do not want to open the GUI and set all the options for all my subjects individually.

So is there any way to extract the current settings as, say, a JSON file so that the key-value pairs could be used to make os.system calls to mrview later on in a script?

Thanks!

Best,
Himanshu

2

MRview has many command-line options that will be processed as if the corresponding action had been performed through the GUI. They can be found at:

https://mrtrix.readthedocs.io/en/latest/reference/commands/mrview.html

or through:

mrview -help
3

Thanks for your response! And sorry, if I wasn’t very clear! I know about the command-line options.

Rather I was just asking if there is a way to extract all the settings and parameter values (that I made in GUI) as a json file so that I can use that json to input the same parameter values in a command-line call. Hope this was more clear.

Thanks again!

4

This is one the many features I would like to implement, but it would require a very substantial re-write of the application. It’s on the wish-list, but it will be a while before I find time to devote to it…

5

I understand the question, I was just hoping that this would already get you most of what you wanted to achieve.

If you set up mrview for one data set and then go over all command line arguments listed in mrview -help and write down all your choices (like view mode, loaded images and their intensity range, colormap, camera settings, text overlay settings, loaded image overlay, their colormap, their transparency and threshold settings, odf settings, fixel settings, tractogram settings, ect, …), one can then easily provide all these choices as command-line parameters in a script. Not every single setting will be scriptable like this, but you can get a long way …

6

You could also look into things like Automator for macOS, which offer a generic solution to what you are trying to achieve. Maybe there are similar tools available for other operating systems?