Hi MRtrix Community,
I’m new to diffusion imaging and just started using MRtrix recently. I ran a dwi2response dhollander command and it works fine, however when I was trying the dwi2response tournier command, I got strange error message:
When I check the detailed processing steps via -debug, I didn’t see any alerting message except the following warning:
How should I solve this issue? Thank you so much in advance!
Best,
Luie
Hi Luie,
I think the warning message in the second output is a red herring; the dwi2response tournier algorithm is configured to always operate on image data from a single b-value, and if it is provided with input data containing multiple b-values, it will automatically select the largest b-value present.
The main issue seems to be that dwi2mask is producing an empty mask. Rather than assessing this within the context of the dwi2response script, you should instead try running dwi2mask directly on your DWI data and see what happens; even run that command with the -debug flag to see if anything unusual pops up. dwi2mask is nowhere near as robust as we would like it to be, but we have been unable to commit resources to implementing something better. Worst case scenario, you can generate a mask yourself and provide that to dwi2response using the -mask option; that way, dwi2response will not need to call dwi2mask to generate a brain mask, as you would be providing it with such a mask explicitly.
Cheers
Rob
Hi Rob,
Making mask through dwi2mask works fine. I ended up providing the mask with dwi2response and it worked. Thank you so much!
Best,
Luie