qsiprep

Preprocessing of diffusion MRI

Science Score: 77.0%

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Links to: zenodo.org
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4 of 25 committers (16.0%) from academic institutions
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Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary

Keywords

bids denoising-images diffusion-mri distortion-correction motion-correction pipelines

Keywords from Contributors

neuroimaging neuroscience interactive magnetoencephalography electroencephalography electrocorticography meg ieeg eeg ecog

Last synced: 6 months ago · JSON representation ·

Repository

Preprocessing of diffusion MRI

Basic Info

Host: GitHub
Owner: PennLINC
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: http://qsiprep.readthedocs.io
Size: 178 MB

Statistics

Stars: 160
Watchers: 12
Forks: 59
Open Issues: 136
Releases: 0

Topics

bids denoising-images diffusion-mri distortion-correction motion-correction pipelines

Created over 7 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Citation

README.rst

.. include:: links.rst

QSIPrep: Preprocessing and analysis of q-space images
=====================================================

.. image:: https://img.shields.io/badge/Source%20Code-pennlinc%2Fqsiprep-purple
  :target: https://github.com/PennLINC/qsiprep
  :alt: GitHub Repository

.. image:: https://readthedocs.org/projects/qsiprep/badge/?version=latest
  :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest
  :alt: Documentation Status

.. image:: https://img.shields.io/badge/docker-pennlinc/qsiprep-brightgreen.svg?logo=docker&style=flat
  :target: https://hub.docker.com/r/pennlinc/qsiprep/tags/
  :alt: Docker

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

.. image:: https://img.shields.io/badge/Nature%20Methods-10.1038%2Fs41592--021--01185--5-purple
  :target: https://doi.org/10.1038/s41592-021-01185-5
  :alt: Publication DOI

.. image:: https://zenodo.org/badge/156589095.svg
  :target: https://doi.org/10.5281/zenodo.14187327
  :alt: Zenodo DOI

.. image:: https://img.shields.io/badge/License-BSD--3--Clause-green
  :target: https://opensource.org/licenses/BSD-3-Clause
  :alt: License


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/PennLINC/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 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 QSIPrep in any way endorse or support this code or its
pipelines**.

Owner

Name: Lifespan Informatics and Neuroimaging Center
Login: PennLINC
Kind: organization

Website: www.pennlinc.io
Repositories: 59
Profile: https://github.com/PennLINC

The Lifespan Informatics and Neuroimaging Center at the University of Pennylvannia

Citation (CITATION.cff)

cff-version: 1.2.0
title: "QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI"
message: If you use this software, please cite it using the following metadata.
type: software
authors:
  - family-names: Cieslak
    given-names: Matthew
    affiliation: Department of Neuropsychiatry, University of Pennsylvania
    orcid: https://orcid.org/0000-0002-1931-4734
  - family-names: Camacho
    given-names: Paul B.
    affiliation: Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, IL, USA
    orcid: https://orcid.org/0000-0001-9048-7307
  - family-names: Covitz
    given-names: Sydney
    affiliation: Perelman School of Medicine, University of Pennsylvania, PA, USA
    orcid: https://orcid.org/0000-0002-7430-4125
  - family-names: Foran
    given-names: William
    affiliation: Department of Psychiatry, University of Pittsburgh Medical Center
    orcid: https://orcid.org/0000-0001-7491-9798
  - family-names: He
    given-names: Xiaosong
    affiliation: Department of Bioengineering, University of Pennsylvania
    orcid: https://orcid.org/0000-0002-7941-2918
  - family-names: Humphries
    given-names: Joseph
    affiliation: Turing Medical
    orcid: https://orcid.org/0000-0002-1025-7956
  - family-names: Legarreta Gorroño
    given-names: Jon Haitz
    affiliation: Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School
    orcid: https://orcid.org/0000-0002-9661-1396
  - family-names: Magnussen
    given-names: Fredrik
    affiliation: Department of Psychology, University of Oslo
    orcid: https://orcid.org/0000-0003-2574-1705
  - family-names: Meisler
    given-names: Steven Lee
    affiliation: Harvard-MIT Program in Speech and Hearing Bioscience and Technology
    orcid: https://orcid.org/0000-0002-8888-1572
  - family-names: Moore
    given-names: Lucille A.
    affiliation: Masonic Institute for the Developing Brain (MIDB), University of Minnesota
    orcid: https://orcid.org/0000-0002-7665-2713
  - family-names: Krause
    given-names: Michael
    affiliation: Max Planck Institute for Human Development, Berlin, Germany
    orcid: https://orcid.org/0000-0002-3878-6542
  - family-names: Sadil
    given-names: Patrick
    affiliation: Johns Hopkins Bloomberg School of Public Health
    orcid: https://orcid.org/0000-0003-4141-1343
  - family-names: Salo
    given-names: Taylor
    email: salot@pennmedicine.upenn.edu
    affiliation: University of Pennsylvania
    orcid: https://orcid.org/0000-0001-9813-3167
  - family-names: Sydnor
    given-names: Valerie Jill
    affiliation: Perelman School of Medicine, University of Pennsylvania
    orcid: https://orcid.org/0000-0002-8640-668X
  - family-names: Satterthwaite
    given-names: Theodore D.
    affiliation: Perelman School of Medicine, University of Pennsylvania, PA, USA
    orcid: https://orcid.org/0000-0001-7072-9399
preferred-citation:
  type: article
  authors:
    - family-names: Cieslak
      given-names: Matthew
    - family-names: Cook
      given-names: Philip A.
    - family-names: He
      given-names: Xiaosong
    - family-names: Yeh
      given-names: Fang-Cheng
    - family-names: Dhollander
      given-names: Thijs
    - family-names: Adebimpe
      given-names: Azeez
    - family-names: Aguirre
      given-names: Geoffrey K.
    - family-names: Bassett
      given-names: Danielle S.
    - family-names: Betzel
      given-names: Richard F.
    - family-names: Bourque
      given-names: Josiane
    - family-names: Cabral
      given-names: Laura M.
    - family-names: Davatzikos
      given-names: Christos
    - family-names: Detre
      given-names: John A.
    - family-names: Earl
      given-names: Eric
    - family-names: Elliott
      given-names: Mark A.
    - family-names: Fadnavis
      given-names: Shreyas
    - family-names: Fair
      given-names: Damien A.
    - family-names: Foran
      given-names: Will
    - family-names: Fotiadis
      given-names: Panagiotis
    - family-names: Garyfallidis
      given-names: Eleftherios
    - family-names: Giesbrecht
      given-names: Barry
    - family-names: Gur
      given-names: Ruben C.
    - family-names: Gur
      given-names: Raquel E.
    - family-names: Kelz
      given-names: Max B.
    - family-names: Keshavan
      given-names: Anisha
    - family-names: Larsen
      given-names: Bart S.
    - family-names: Luna
      given-names: Beatriz
    - family-names: Mackey
      given-names: Allyson P.
    - family-names: Milham
      given-names: Michael P.
    - family-names: Oathes
      given-names: Desmond J.
    - family-names: Perrone
      given-names: Anders
    - family-names: Pines
      given-names: Adam R.
    - family-names: Roalf
      given-names: David R.
    - family-names: Richie-Halford
      given-names: Adam
    - family-names: Rokem
      given-names: Ariel
    - family-names: Sydnor
      given-names: Valerie J.
    - family-names: Tapera
      given-names: Tinashe M.
    - family-names: Tooley
      given-names: Ursula A.
    - family-names: Vettel
      given-names: Jean M.
    - family-names: Yeatman
      given-names: Jason D.
    - family-names: Grafton
      given-names: Scott T.
    - family-names: Satterthwaite
      given-names: Theodore D.
  doi: 10.1038/s41592-021-01185-5
  journal: Nature Methods
  start: 775
  end: 778
  title: 'QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data'
  issue: 7
  volume: 18
  year: 2021
repository-code: 'https://github.com/PennLINC/qsiprep'
url: 'https://qsiprep.readthedocs.io'
keywords:
  - neuroimaging
  - workflow
  - pipeline
  - preprocessing
  - dMRI
  - BIDS
  - BIDS-App
license: BSD-3-Clause
version: 1.0.0rc1
date-released: '2024-11-19'

GitHub Events

Total

Create event: 58
Release event: 4
Issues event: 109
Watch event: 20
Delete event: 66
Member event: 2
Issue comment event: 246
Push event: 266
Pull request review comment event: 92
Pull request review event: 115
Pull request event: 108
Fork event: 4

Last Year

Create event: 58
Release event: 4
Issues event: 109
Watch event: 20
Delete event: 66
Member event: 2
Issue comment event: 246
Push event: 266
Pull request review comment event: 92
Pull request review event: 115
Pull request event: 108
Fork event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 538
Total Committers: 25
Avg Commits per committer: 21.52
Development Distribution Score (DDS): 0.264

Past Year

Commits: 150
Committers: 13
Avg Commits per committer: 11.538
Development Distribution Score (DDS): 0.333

Top Committers

Name	Email	Commits
Matt Cieslak	m**k@g**m	396
jbh1091	j**s@f**o	100
Philip Cook	c**a@p**u	6
Jon Haitz Legarreta Gorroño	j**a@g**m	5
John Kruper	3****0	3
Valerie Jill Sydnor	v**r@g**m	3
Will Foran	w**n@g**m	2
Steven Meisler	s**r@g**u	2
pcamach2	4****2	2
Pierre	6****c	2
j-bourque	4****e	2
Shreyas Fadnavis	s**s@g**m	2
Shreyas Fadnavis	s**n@i**u	1
Fredrik Magnussen	f**a@g**m	1
dependabot[bot]	4****]	1
Sydney Covitz	7****z	1
Taylor Salo	t**0@g**m	1
arovai	8****i	1
Ariel Rokem	a**m@g**m	1
Hamsi Radhakrishnan	3****n	1
Michael	k**e@m**e	1
Michael	mk@g****s	1
Tinashe Michael Tapera	t**a@g**m	1
nseider	1****r	1
Adam Richie-Halford	r****d	1

Committer Domains (Top 20 + Academic)

galax.is: 1 mpib-berlin.mpg.de: 1 iu.edu: 1 g.harvard.edu: 1 pennmedicine.upenn.edu: 1 firmm.io: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 339
Total pull requests: 221
Average time to close issues: 10 months
Average time to close pull requests: about 2 months
Total issue authors: 127
Total pull request authors: 24
Average comments per issue: 3.19
Average comments per pull request: 1.48
Merged pull requests: 180
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 74
Pull requests: 70
Average time to close issues: 26 days
Average time to close pull requests: 5 days
Issue authors: 28
Pull request authors: 9
Average comments per issue: 1.26
Average comments per pull request: 1.46
Merged pull requests: 59
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

mattcieslak (61)
tsalo (35)
araikes (26)
jhauneuro (15)
WilliamFCB (10)
smeisler (10)
arokem (9)
dyhan316 (9)
jhlegarreta (7)
cookpa (7)
dkp (6)
pierre-nedelec (6)
psadil (5)
julfou81 (5)
weiwei-wch (5)

Pull Request Authors

mattcieslak (141)
tsalo (117)
arokem (12)
smeisler (10)
jhlegarreta (7)
cookpa (6)
jbh1091 (5)
LuciMoore (4)
araikes (4)
chiuhoward (4)
pierre-nedelec (3)
psadil (3)
36000 (3)
valeriejill (3)
effigies (2)

Top Labels

Issue Labels

bug (89) enhancement (48) documentation (5) question (4) breaking-change (4) maintenance (3) refactor (2) ignore-for-release (1)

Pull Request Labels

bug (35) maintenance (28) documentation (21) breaking-change (20) refactor (14) enhancement (9) ignore-for-release (8) testing (7) dependencies (1)

Packages

Total packages: 1
Total downloads:
- pypi 470 last-month
Total docker downloads: 203

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 55
Total maintainers: 1

pypi.org: qsiprep

qsiprep builds workflows for preprocessing and reconstructing q-space images

Homepage: https://github.com/pennlinc/qsiprep
Documentation: https://www.qsiprep.readthedocs.io
License: Copyright (c) 2015-2018, the BBL developers team. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of qsiprep nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Latest release: 1.0.1
published 11 months ago

Versions: 55
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 470 Last month
Docker Downloads: 203

Rankings

Docker downloads count: 3.0%

Forks count: 5.9%

Stargazers count: 6.7%

Dependent packages count: 10.1%

Average: 10.6%

Downloads: 16.1%

Dependent repos count: 21.6%

Maintainers (1)

mcieslak

Last synced: 7 months ago

Dependencies

.readthedocs/environment.yaml conda

pip >=20.1
python 3.7.*
python-spams <=2.6.1

docs/requirements.txt pypi

CommonMark ==0.7.5
mock *
nbsphinx *
numpy *
pydot >=1.2.3
pydotplus *
sphinx-argparse ==0.2.1

requirements.txt pypi

dipy ==1.0.0
grabbit ==0.2.3
nipype ==1.2.0
pybids >=0.11.1
sentry_sdk ==0.13.1
svgutils ==0.3.0
versioneer *

docs/environment.yml conda

cython
funcsigs
future
jinja2 2.8.*
matplotlib 2.0.0.*
mock
networkx >=2.0.0
nibabel
nipype >=1.1.1
numpy >=1.11.0
pydot >=1.2.3
python 3.5
python-dateutil
scikit-learn 0.18.1.*
scipy 0.18.1.*
sphinx >=1.5.1
sphinx_rtd_theme
traits 4.6.*
xvfbwrapper

Dockerfile docker

pennbbl/qsiprep_build 22.10.5 build