Hi MRtrix community,
I have been working with MRtrix for a while now and just got an error that I have never seen before. In the screenshot of my terminal down below you can see the error and the line I am trying to run.
The data consists of 16 gradient directions of b=1000 and a b=0 image. I suppose something is wrong with this data set, since I have used the exact same command with different data sets. Even stranger is that this dwi data(sub13_3split2_den_degibbs_preproc_unbias.mif) is extracted from a original scan that consisted of 32 gradient directions and was split in half due to scarcity of subjects and that the dwi2response dhollander command works perfectly fine for the other half of the data.
I am not entirely sure what the errors are saying. What could be the cause of the error?
Thanks in advance,
Youri
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It looks to me like the command failed due to no white matter voxels making it to the final selection. You can see that the refined WM mask includes only 76 voxels, which then gets refined to 0.5% of that number, which would round down to zero…
Looking further up, it looks like the original mask is far too restrictive, only containing 4,479 voxels, where we’d be expecting in the region of 100,000. I’m not sure why that might be, but if you already have a more sensible brain mask, I suggest you try passing that to dwi2response using the -mask option, see if that helps to resolve the issue.
Thank you!
I had a better mask and using the -mask option did help.
I also generated a new mask myself with the data I used for the dwi2repsonse command and for some reason it generated a mask only including voxels around the corpus callosum
