QSIprep: Preprocessing and analysis of q-space images

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Full documentation at https://qsiprep.readthedocs.io


qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data. The main features of this software are

  1. A BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.

  2. Automatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, coregister and resample your scans, producing visual reports and QC metrics.

  3. A system for running state-of-the-art reconstruction pipelines that include algorithms from Dipy, MRTrix, DSI Studio and others.

  4. A novel motion correction algorithm that works on DSI and random q-space sampling schemes



The preprocessing pipelines are built based on the available BIDS inputs, ensuring that fieldmaps are handled correctly. The preprocessing workflow performs head motion correction, susceptibility distortion correction, MP-PCA denoising, coregistration to T1w images, spatial normalization using ANTs and tissue segmentation.


The outputs from the Preprocessing pipelines can be reconstructed in many other software packages. We provide a curated set of Reconstruction Workflows in qsiprep that can run ODF/FOD reconstruction, tractography, Fixel estimation and regional connectivity.


The qsiprep pipeline uses much of the code from FMRIPREP. It is critical to note that the similarities in the code do not imply that the authors of FMRIPREP in any way endorse or support this code or its pipelines.