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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
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mrconvert parcRGB.mif ... Error when using parcellation=perry512 #57

Closed paul-triebkorn closed 3 years ago

paul-triebkorn commented 5 years ago

Hi developers Thanks for the nice container.

I just encountered a minor issue. When running the container with --parcellation perry512 and --output_verbosity 3, the container generates an error at the last steps.

mrtrix3_connectome.py: [ERROR] Command failed: mrconvert parcRGB.mif /mrtrix3_out/sub-QL20120814/anat/sub-QL20120814_parc-perry512_colour.nii.gz -strides +1,+2,+3 (mrtrix3_connectome.py:797) mrtrix3_connectome.py: Output of failed command: mrconvert: [INFO] opening image "parcRGB.mif"... mrconvert: [ERROR] failed to open key/value file "parcRGB.mif": No such file or directory mrconvert: [ERROR] error opening image "parcRGB.mif"

I assume this is because "parcRGB.mif" is not created on line 650 in mrtrix3_connectome.py, cause mrtrix_lut_file is empty for the specified parcellation. However on line 797 mrconvert tries to use that ".mif" file and thus generates the Error.

best Paul

Lestropie commented 5 years ago

Hi Paul,

Good catch. Suppose this sort of thing is why many softwares rely on comprehensive CI testing matrices to stress-test all possible combinations of parameters...

I've not been able to put the time into this tool I'd like to, with the MRtrix3 workshop last week and now trying to get that software released; but I'll try to put a fix for this together with some of the other changes I've been making and push a new version.

Rob