[feature request] final gradient files from dwigradcheck

[smeisler]

Hi,

I think it would be valuable if the QSIPrep output .b/.bvec/.bval files come from dwigradcheck. I think not a lot of people know that some scanners outputs may have to flip certain vectors to be used in certain analyses (e.g. Siemens often has to have x-axis flipped). Exporting corrected gradient tables leaves the guess work out of it.

Thanks, Steven

[mattcieslak]

I think it should be the responsibility of the person who does BIDS curation on the data to make sure that the gradients match the images. QSIPrep doesn't run dwigradcheck in the preprocessing workflow and the bvecs you get out will correspond to the bvecs you put in (with the .b file for mrtrix).

The safest way to make sure your bvecs are interpreted correctly is to reorient the image to LAS+/RPI/FSL standard orientation and then use dwigradcheck with the original bvecs. Use the LAS+/RPI/FSL image in your BIDS data and along with the corrected bvecs from dwigradcheck.

Until BIDS approves the RASB format for gradients we are stuck with the tricky FSL bvec format