https://github.com/PennLINC/qsiprep_build

Builds the dependencies for qsiprep
https://github.com/PennLINC/qsiprep_build

Last synced: 3 months ago
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Builds the dependencies for qsiprep

• Host: GitHub
• URL: https://github.com/PennLINC/qsiprep_build
• Owner: PennLINC
• License: apache-2.0
• Created: 2021-11-15T19:57:20.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-07-22T14:29:01.000Z (4 months ago)
• Last Synced: 2024-07-22T17:25:31.006Z (4 months ago)
• Language: Dockerfile
• Size: 32.1 MB
• Stars: 2
• Watchers: 5
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
.. include:: links.rst

QSIprep: Preprocessing and analysis of q-space images

=======================================================

.. image:: https://readthedocs.org/projects/qsiprep/badge/?version=latest

  :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest

  :alt: Documentation Status

.. image:: https://circleci.com/gh/PennLINC/qsiprep/tree/master.svg?style=svg

  :target: https://circleci.com/gh/PennLINC/qsiprep/tree/master

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

.. 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**.