I am trying to do preprocessing and reconstruction on minimally preprocessed ABCD dwi data, which I was told, already had eddy and TOPUP done on them.
I want to configure qsiprep so that those two are not applied, but cannot find the right command to do so:
In the image above in qsiprep docs, I thought that the first method could be used, but found that the first method still performs eddy. Is there a way to disable FSL based dwi preprocessing completely?
I’m not sure QSIprep will be the best tool for you. Other steps such as denoising are supposed to be done before Eddy/TOPUP, so trying to run qsiprep on data with these steps already done is going to be problematic. I would either 1) preprocess the raw data, or 2) wait for the next ABCD-BIDS Collection 3165 Preprocessed Data Release, which will include QSIPrep outputs. Collection 3165 - ABCD-BIDS Community Collection (ABCC)
Thank you for the reply! I looked at the link you sent me, but it seems that their latest release was two years ago, so I think that I should preprocess the raw data. Thank you for the insight