Thank you @maxpietsch .
I’m still stuck with your sample. I think the important part (the actual python sample) is this one, right? I try to reproduce this in my script but I have this error
Cannot find reference ‘app’ in ‘mrtrix3.py’
Even before I tried your method, i was (i think) able to load the mrtrix3.py module into my python script by following the instructions here
However, like I mentioned above, the mrtrix3 module doesn’t contain a lot of the attributes that you reference in your script, like app, image, path, or run. I’m not sure if that means that the import is not working properly. as far as I can debug it, it is returning success. In my mrtrix3 modules I only see
Unfortunately, running your bash script also failed when it tried to compile mrtrix after cloning it. It complains about Eigen3 in ./configure -noshared -nogui and I don’t want to go down the route of recompiling mrtrix, i’m sure that the precompiled version can still be used in python, right?
So I can think of two things
- My import is not working properly and it’s not bringing everything that the mrtrix python module has to offer and that your sample
mralign.pyis using - your sample script was importing a different version of the mrtrix3 python module that has changed now but because you are checking out
masterin your bash script, it doesn’t work any more
thanks for any pointers. and while at it, is there any documentaiton of what’s inside the mrtrix python module? how did you know about mrtrix3.app, mrtrix3.run, etc