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QSIPrep: Preprocessing and analysis of 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.
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

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.. _preprocessing_def:

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_def:

Reconstruction

The outputs from the :ref:preprocessing_def pipelines can be reconstructed in many other software packages. We recommend passing QSIPrep derivatives along to QSIRecon <https://qsirecon.readthedocs.io/en/latest/>_, 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 QSIPrep in any way endorse or support this code or its pipelines.