How to make mask2glass available?

MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density

http://www.mrtrix.org

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How to make mask2glass available? #2883

Open legendaddy4552 opened 5 months ago

legendaddy4552 commented 5 months ago

I want to use mask2glass but It is not available on my system.

I looked for mask2glass discussions but I dont know how to obtain the file and make it available on my system.

I am kind a new with these stuffs and I will be very happy If someone can tell me how to import these external commands

Lestropie commented 5 months ago

mask2glass is not yet included in a tagged release; it is only present on the development branch here.

You can either:

Clone that branch and compile (noting that the compilation instructions for dev are substantially different to that of 3.0.x
Just download the file linked above and save it to the bin/ directory of your existing MRtrix3 install; there's a good chance that'll work without modification.

legendaddy4552 commented 5 months ago

I got the following error, is there a problem about python installation? If so I am using MNE package of python on my Ubuntu, there shouldnt be a problem with that

Lestropie commented 5 months ago

The script expects as input a 3D image (even though the command is called "mask*", it technically doesn't have to be bitwise). The fact you're providing a 4D image series is tripping up the internal operations. I'll need to add a check to the script so that it produces a more sensible error message.