QSIPrep: Preprocessing of Diffusion MRI (q-space) Images

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

About

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. The plan for a dataset can be previewed before running with qsiplan.

  3. Head motion and eddy-current correction for any sampling scheme, including DSI and compressed sensing, with FSL’s eddy or TORTOISE DIFFPREP.

https://github.com/PennLINC/qsiprep/raw/main/docs/_static/workflow_full.svg

Preprocessing

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.

Reconstruction

The outputs from the Preprocessing pipelines can be reconstructed in many other software packages. We recommend passing QSIPrep derivatives along to QSIRecon, which provides a curated set of reconstruction workflows that can run ODF/FOD reconstruction, tractography, Fixel estimation and regional connectivity.

Note

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.