Include option to disable bvalue scaling

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

http://micapipe.readthedocs.io

GNU General Public License v3.0

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Include option to disable bvalue scaling #62

Closed ajschadler12 closed 1 year ago

ajschadler12 commented 1 year ago

What is the current behaviour?
Micapipe uses default behavior of mrconvert, which includes bvalue scaling.
What is the motivation / use case for changing the behaviour?
For ABCD multishell RSI sequences, bvalue-scaling leads to incorrect DTI estimation. Allowing for an option to not scale bvalues in mrconvert would make the DTI pipeline much more flexible.

rcruces commented 1 year ago

Hello, thank you for the observation, could you please provide us with the command that would not apply the rescaling or the bvalues? or are you referring to the BZeroThreshold used in the processing? because indeed the default BZeroThreshold is set to 61 but this behaviour could be customize. thank you

ajschadler12 commented 1 year ago

Hi, yes, you will need to append -bvalue_scaling no to mrconvert when initially converting from nifti to mif. E.g.

mrconvert -bvalue_scaling no -fslgrad sub-abcd_ses-01_dir-AP_dwi.bvec sub-abcd_ses-01_dir-AP_dwi.bval sub-abcd_ses-01_dir-AP_dwi.nii.gz sub-abcd_ses-01_dir-AP_dwi.mif

In case you were curious, Dr. Tournier left an in-depth comment on why bvalue scaling might fail in some settings, particularly our data.

rcruces commented 1 year ago

Thank you for the observation, we added this feature on the latest v0.1.5 version of the pipeline this week. We are still building a new docker container updated.

rcruces commented 1 year ago

The docker was successfully built and this option is include in the versions v0.1.5 and v0.2.0