Hi all,
I’m using QSIPrep to preprocess some DWI scans and I just realized that QSIPrep has their own method for choosing b=0 volumes for SDC. For example, I have four EPI fieldmaps (AP, PA, AP, PA). For each of their JSON files, I specified an “IntendedFor” sidecar for a single DWI scan ¶:
But when I checked the /hmc_sdc_wf/gather_inputs/b0_selection_info.tsv file, I noticed that only 3 volumes were selected for SDC. One volume from the DWI, and two other volumes from the AP fieldmaps.
I understand that QSIPrep is finding the most representative b=0 images, but is there a way to force it to use all the fieldmaps that I intended for it to use? One reason for this is because I have my own diffusion preprocessing pipeline that does this and I want to compare the results with QSIPrep.
Any help would be appreciated. Thank you! Also am new to Neurostars, apologies for any formatting issues.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Can confirm - there’s no way to change this behavior via options. The reason we limit it is because every additional volume given to topup exponentially increases the run time. Plus, including noisy b=0s actively downgrades the quality of the estimated field.
Sorry @Steven@mattcieslak I also just wanted more clarification on why only 3 volumes were picked, instead of an even number of volumes. Referring to my previous example, QSIPrep picked a b=0 volume from the DWI scan ¶ and 2 b=0 volumes from 2 fieldmaps- both AP. Why does it not just pick 2, or 4? Why an odd number? I think I still don’t fully understand how QSIPrep picks its b=0 volumes.