qsiprep
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Preprocessing and reconstruction of diffusion MRI
.. include:: links.rst
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
- A BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.
- Automatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, coregister and resample your scans, producing visual reports and QC metrics.
- A system for running state-of-the-art reconstruction pipelines that include algorithms
from Dipy_, MRTrix_,
DSI Studio
_ and others. - A novel motion correction algorithm that works on DSI and random q-space sampling schemes
.. image:: https://github.com/PennBBL/qsiprep/raw/master/docs/_static/workflow_full.png
.. _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 provide a curated set of :ref:recon_workflows
in qsiprep
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.