I’m planning to use minimally processed diffusion MRI data in QSIprep to finish off processing and conduct tractography. The problem is that the ABCD dMRI data (3 files per participant - NII, JSON, bvecs, bvals) has already gone through some processing steps by the ABCD team, such as correction for motion, distortions, and eddy currents (Image processing and analysis methods for the Adolescent Brain Cognitive Development Study). We’re finding it difficult to bypass some of the processing steps in QSIprep, such as bypassing eddy current corrections and motion correction (perhaps through a null configuration file?). Any advice would be much appreciated, as both ABCD and QSIprep are amazing resources, and it’d be great to combine the two!
At the moment I don’t think it’s possible to just reconstruct the preprocessed ABCD data from NDA. We’d recommend running the full QSIPrep preprocessing and reconstruction workflows on the BIDS data in the ABCC.
Also, depending on your timeline, there will be QSIPrep preprocessed data in release 2.0 which you can easily run the reconstruction-only pipeline on.
Just following on this thread, do you know when the QSIprep 2.0 will be released?
I don’t know for sure but is likely on the order of months from now.
Just wanted to check: has the ABCD diffusion data you have access to been properly converted to BIDS? That is, the reverse-PE (blip-down) image has been properly extracted and the multishell DWI has correct bval/bvec?