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MRdataset

MRdataset : A unified and user-friendly interface to medical imaging datasets - Published in JOSS (2024)

https://github.com/open-minds-lab/mrdataset

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

mri neuroimaging neuroscience niqc quality-control

Keywords from Contributors

biomedical data-integration data-structures datascience datastructures machine-learning-workflows medical-data neuroinformatics userfriendly
Last synced: 6 months ago · JSON representation

Repository

MRdataset : unified interface to various neuroimaging dataset formats

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 4
  • Open Issues: 13
  • Releases: 0
Topics
mri neuroimaging neuroscience niqc quality-control
Created almost 4 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

=====================================================================
MRdataset : unified interface to various neuroimaging dataset formats
=====================================================================

.. image:: https://img.shields.io/pypi/v/MRdataset.svg
        :target: https://pypi.python.org/pypi/MRdataset

.. image:: https://app.codacy.com/project/badge/Grade/4e6e129acb3340e3b422541be3924a90
        :target: https://app.codacy.com/gh/sinhaharsh/MRdataset/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade

.. image:: https://github.com/sinhaharsh/MRdataset/actions/workflows/continuous-integration.yml/badge.svg
        :target: https://github.com/sinhaharsh/MRdataset/actions/workflows/continuous-integration.yml


.. image:: ./docs/images/hierarchy.jpg

Description
------------

* Provides a unified interface for horizontal and vertical traversal of various neuroimaging datasets (DICOM) and any other generic format etc.
* Ensures that the DICOM files are valid imaging DICOMs and provides the option to skip phantoms, localizer, head scouts etc.
* Provides flexibility to ignore automatically generated derived scans such as MoCo series, Single-band references, perfusion weighted scans.
* Verifies if each DICOM slice belongs to the same scan volume and, then subsequently organizes all scans are hierarchical fashion (Subject > Session > Sequence > Run)
* Identifies sequences acquired within the same session, which is especially useful for associating field maps with their corresponding functional (EPI) scans.


Documentation 
-------------

https://open-minds-lab.github.io/MRdataset/

Owner

  • Name: Open Minds
  • Login: Open-Minds-Lab
  • Kind: organization
  • Email: openmindslab@gmail.com

Open minds in machine learning, informatics and data science

JOSS Publication

MRdataset : A unified and user-friendly interface to medical imaging datasets
Published
March 21, 2024
DOI
Volume 9, Issue 95, Page 6269
Authors
Harsh Sinha ORCID
Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, United States of America
Pradeep Reddy Raamana ORCID
Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, United States of America, Department of Biomedical Informatics, University of Pittsburgh, United States of America, Department of Radiology, University of Pittsburgh, United States of America
Editor
Marcel Stimberg ORCID
Tags
neuroimaging
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GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 860
  • Total Committers: 3
  • Avg Commits per committer: 286.667
  • Development Distribution Score (DDS): 0.02
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Harsh Sinha h****a@p****u 843
Pradeep Reddy Raamana r****a@g****m 15
WillForan w****n@g****m 2
Committer Domains (Top 20 + Academic)
pitt.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 17
  • Total pull requests: 15
  • Average time to close issues: 25 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 4
  • Total pull request authors: 5
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.73
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sinhaharsh (11)
  • htwangtw (3)
  • djmannion (2)
  • raamana (1)
Pull Request Authors
  • sinhaharsh (19)
  • mstimberg (2)
  • yarikoptic (1)
  • raamana (1)
  • WillForan (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 27 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: mrdataset

MRdataset

  • Homepage: https://github.com/Open-Minds-Lab/MRdataset
  • Documentation: https://open-minds-lab.github.io/MRdataset/
  • License: Apache Software License 2.0 Copyright (c) 2022, Pradeep Raamana Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
  • Latest release: 0.4.4
    published almost 2 years ago
  • Versions: 7
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 27 Last month
Rankings
Dependent packages count: 3.3%
Forks count: 19.2%
Dependent repos count: 22.3%
Average: 24.5%
Downloads: 38.9%
Stargazers count: 38.9%
Maintainers (1)
openmindslab
Last synced: 6 months ago

Dependencies

requirements_dev.txt pypi
  • dicom2nifti >=2.4.2 development
  • dictdiffer * development
  • nibabel * development
  • pandas * development
  • pybids * development
  • pydicom * development
.github/workflows/continuous-integration.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
pyproject.toml pypi
  • dicom2nifti >=2.4.2
  • nibabel *
  • numpy *
  • protocol *
  • pydicom *