Mrinfo UNKOWN option -shell_indices


I just updated my MRtrix version.
Im trying to use:

dwifslpreproc dwi_preproc2.mif dwi_preproc3.mif -rpe_none -pe_dir AP

And I’m getting the following error when running the script:

mrinfo UNKOWN option -shell_indices
mrinfo: **[ERROR] unknown option "-shell_indices"**

dwifslpreproc: **[ERROR] Unhandled Python exception:**

dwifslpreproc: **[ERROR]** *ValueError: invalid literal for int() with base 10: ''*

dwifslpreproc: **[ERROR] Traceback:**

dwifslpreproc: **[ERROR]** */Users/miguel/mrtrix3/bin/dwifslpreproc:321 (in execute())*

dwifslpreproc: **[ERROR]** *shell_indices = [ [ int(i) for i in entry.split(',') ] for entry in image.mrinfo('dwi.mif', 'shell_indices').split(' ') ]*

Same error when only running

mrinfo -shell_indices (image)

Any help or comment would be appreciated.


It sounds to me like the dwifslpreproc script is using an old version of mrinfo for some reason. This shouldn’t be happening, given the safeguards in place to ensure that the scripts always invoke the commands from the exact same location as the script itself, precisely to avoid these kinds of issues.

The only thing I can think of is that you might have updated your git repo with a git pull, but forgot to run ./configure && ./build to re-compile the executables? In this case, you’d have up to date versions of the scripts (they don’t need to be recompiled), but old versions of the C++ binaries. Try re-building, see if that fixes the issue.

Thank you, that did it.

Sorry I missed that part. I’m new to this but the website and community have been really helpful.

It’s an admirable work.