The qsiprep preprocessing workflow takes as principal input the path of the dataset that is to be processed. The input dataset is required to be in valid BIDS formate at least one diffusion MRI series. The T1w image and the DWI may be in separate BIDS <session> folders for a given subject. We highly recommend that you validate your dataset with the free, online BIDS Validator.

The exact command to run qsiprep depends on the Installation method. The common parts of the command are similar to the BIDS-Apps definition. Example:

qsiprep data/bids_root/ out/ participant -w work/

Command-Line Arguments

The docker wrapper CLI

The singularity wrapper CLI

Note on using CUDA

The CUDA runtime version 9.1 is included in the QSIPrep docker image. The CUDA version of eddy is dramatically faster than the openmp version. Information on running Docker with CUDA enabled can be found on dockerhub. If running with singularity, the call to singularity should include --nv. To enable CUDA, see Configuring eddy.


Logs and crashfiles are outputted into the <output dir>/qsiprep/sub-<participant_label>/log directory. Information on how to customize and understand these files can be found on the nipype debugging page.

CUDA Support

As of version 0.6.7 CUDA version 9.1 is supported in the QSIPrep container! To run locally using docker you will need the nvidia container runtime installed for Docker version 19.0.3 or higher. Singularity images will run with CUDA 9.1 with the -nv flag.

Support and communication

The documentation of this project is found here:

All bugs, concerns and enhancement requests for this software can be submitted here: