Qsiprep Preprocessing Issue

There seems to be an issue with qsiprep’s output. The eddy and topup-corrected output doesn’t look preprocessed (see figures below).

Relevant info:

  • qsiprep version: 0.18.0alpha0
  • qsiprep command: /usr/local/miniconda/bin/qsiprep /path/to/BIDS/ /path/to/BIDS/derivatives/ participant --participant-label sub-X -w /path/to/qsiprep/work --fs-license-file /path/to/license.txt --hmc-transform Rigid --pepolar-method TOPUP --output-resolution 2

Is qsiprep being run correctly with the above command?

Hi @ameenq05,

You should use the latest version to ensure there’s not an issue that’s already been addressed. What in particular are you worried about? If it’s the distortions, have you confirmed SDC was performed? Is it possible phase encoding directions were not correctly specified?

Best,
Steven