A problem of running extented script

When I running this script, occurred an error:

How to deal with this?

Dear fxg,

This is an external script that is using the MRtrix3 Python API from two years ago. In the meanwhile, this API has changed and the script, being external, has not been updated accordingly.

You can deal with this in several ways:

  • Use an outdated MRtrix3 version that still uses the python API that this script was originally written for. This means checking out an MRtrix3 version that dates back two years and build it from the source. This is probably not the recommended solution and definitely not a long-term solution.

  • Port the script to use the new API. If you know your way around Python, it should be possible to port this script by looking at up-to-date scripts that live in MRtrix3’s bin folder. One that is easy to look at is https://github.com/MRtrix3/mrtrix3/blob/master/bin/dwishellmath

  • If you are lucky, @rsmith, the original author of the script, might have an updated version of the script available.

Thanks for your suggestions.
The second method seems like to be a better option. But I’m a clinical medicine student, I have no knowledge of programming. I don’t know how to do this, if I just copy “dwishellmath” file to MRtrix3’s bin folder? So, can you tell me how to do this in detail?
Thanks for your help again.

It should already be there if you are using the latest version. But if you have no knowledge of programming, I would not bother trying to port it yourself…

Hi @fxg,

Thanks for the report; I will try to find the opportunity to port this standalone script to the updated Python API that was part of the 3.0.0 update.



The maskconnectivity Gist has been updated to work with the MRtrix3 production release.


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Thanks for your working! It’s a great help to my project.