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"No b=0 volumes present" when bvals are under b0 threshold but not 0 #703
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Great catch! thanks for reporting. Should be an easy fix |
@teresamg do you have the error message from this? I'm wondering where this dwiextract is being run |
Here is the full output from the error (sorry for the formatting):
|
could you try pennbbl/qsiprep:unstable? |
Same error |
I tried adding a
In the long run I think qsiprep will have to write the mrtrix config file into the derivatives and set an environment variable to point to it |
Okay I built a .sif, echoed "BZeroThreshold: 100" to ~/.mrtrix.conf inside of it, and it ran without errors! |
Any chance it would help to change DWIBiasCorrectInputSpec in qsiprep/interfaces/mrtrix.py from
to
or workflow in qsiprep/config.py from Should there be another use somewhere of |
Summary
I am receiving the following error from dwibiascorrect when the lowest bvals are not 0, but below the b0 threshold:
In this case the lowest bvals are 10. Explicitly setting --b0-threshold to 100 or using --no-b0-harmonization does not resolve the error, but manually changing the 10s to 0s in *.bval does resolve the error.
Additional details
Reproducing the bug
Terminal command (without full paths):
These are the bvals:
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