qsirecon

Reconstruction of preprocessed q-space images (dMRI)

https://github.com/pennlinc/qsirecon

Science Score: 67.0%

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Academic email domains
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Institutional organization owner
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Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Keywords

bids bids-apps bids-format bidsapp diffusion-mri dmri dwi mri

Last synced: 6 months ago · JSON representation ·

Repository

Reconstruction of preprocessed q-space images (dMRI)

Basic Info

Host: GitHub
Owner: PennLINC
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://qsirecon.readthedocs.io/
Size: 179 MB

Statistics

Stars: 12
Watchers: 4
Forks: 12
Open Issues: 71
Releases: 5

Topics

bids bids-apps bids-format bidsapp diffusion-mri dmri dwi mri

Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Citation

README.rst

.. include:: links.rst

##############################################################
QSIRecon: Reconstruction of preprocessed q-space images (dMRI)
##############################################################

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

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

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

.. image:: https://circleci.com/gh/PennLINC/qsirecon/tree/main.svg?style=svg
  :target: https://circleci.com/gh/PennLINC/qsirecon/tree/main
  :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/DOI/10.5281/zenodo.14193616.svg
  :target: https://doi.org/10.5281/zenodo.14193616
  :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://qsirecon.readthedocs.io

*****
About
*****

QSIRecon builds post-processing workflows that produce many of the biologically-interesting dMRI
derivatives used for hypothesis testing. The main goal of QSIRecon is to make the state-of-the-art
methods available in Dipy_, MRTrix_, `DSI Studio`_, PyAFQ_  and other software packages easy to apply on
preprocessed dMRI data. QSIRecon is companion software for `XCP-D `_,
doing for dMRI what XCP-D does for BOLD.

QSIRecon workflows can produce outputs such as

 * ODF/FOD reconstruction
 * Model fits and parameter estimation
 * Tractography
 * Tractometry
 * Regional connectivity
 * Tabular data

.. image:: https://github.com/PennLINC/qsirecon/raw/main/docs/_static/workflow_full.png

***************
Citing QSIRecon
***************

If you use QSIRecon in your research, please use the boilerplate generated by the workflow.
The main citation is

  Cieslak, M., Cook, P. A., He, X., Yeh, F. C., Dhollander, T., Adebimpe, A.,
  ... & Satterthwaite, T. D. (2021). QSIPrep: an integrative platform for preprocessing
  and reconstructing diffusion MRI data. Nature methods, 18(7), 775-778.

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: "QSIRecon: Reconstruction of preprocessed q-space images (dMRI)"
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: Krause
    given-names: Michael
    affiliation: Max Planck Institute for Human Development, Berlin, Germany
    orcid: https://orcid.org/0000-0002-3878-6542
  - 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: Raikes
    given-names: Adam
    affiliation: Center for Innovation in Brain Science, University of Arizona
    orcid: https://orcid.org/0000-0002-1609-6727
  - family-names: Rauland
    given-names: Amelie
    affiliation: Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
    orcid: https://orcid.org/0000-0002-8095-2073
  - 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/qsirecon'
url: 'https://qsirecon.readthedocs.io'
keywords:
  - neuroimaging
  - workflow
  - pipeline
  - postprocessing
  - reconstruction
  - dMRI
  - BIDS
  - BIDS-App
license: BSD-3-Clause
version: 1.1.1
date-released: '2025-08-18'

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 27
Total pull requests: 27
Average time to close issues: 4 months
Average time to close pull requests: 2 days
Total issue authors: 12
Total pull request authors: 7
Average comments per issue: 0.52
Average comments per pull request: 0.78
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 26
Pull requests: 27
Average time to close issues: about 1 month
Average time to close pull requests: 2 days
Issue authors: 12
Pull request authors: 7
Average comments per issue: 0.38
Average comments per pull request: 0.78
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

tsalo (37)
mattcieslak (22)
araikes (10)
smeisler (10)
samuelholly (3)
dkp (3)
chrisadamsonmcri (2)
chiuhoward (2)
LuRoe7 (2)
akelkar26 (2)
layerConnectome (1)
Xinquan-Lu (1)
Shade- (1)
jhauneuro (1)
j1c (1)

Pull Request Authors

tsalo (61)
mattcieslak (30)
dependabot[bot] (11)
smeisler (9)
araikes (4)
ameliecr (2)
chiuhoward (2)
arokem (2)
hfxcarl (1)
LuciMoore (1)
dkp (1)
pcamach2 (1)
cookpa (1)
36000 (1)

Top Labels

Issue Labels

enhancement (48) bug (33) question (3) documentation (2) maintenance (2) testing (1)

Pull Request Labels

bug (22) maintenance (21) ignore-for-release (18) breaking-change (12) enhancement (12) documentation (8) refactor (4) testing (2)

Dependencies

.github/workflows/lint.yml actions

actions/checkout v4 composite
actions/setup-python v5 composite

Dockerfile docker

pennlinc/qsirecon_build 24.7.4 build
python slim build

pyproject.toml pypi

SimpleITK *
dipy >=1.8.0,<1.9.0
dmri-amico == 1.5.4
fury *
importlib_resources python_version < "3.11"
indexed_gzip <= 1.8.7
jinja2 < 3.1
matplotlib *
networkx ~= 2.8.8
nibabel <= 5.2.0
nilearn == 0.10.1
nipype == 1.8.6
niworkflows >=1.9,<= 1.10
numpy <= 1.26.3
pandas < 2.0.0
psutil <= 5.9.8
pyAFQ == 1.3.2
pybids *
pyyaml *
scikit-image *
scikit-learn <= 1.4.0
seaborn *
sentry_sdk *
svgutils <= 0.3.4
transforms3d *
vtk *
xvfbwrapper *

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