Data

Tools

Indexes

Applications

Experiments

Open Source Science

sdc-bids-intromri

Introduction to MRI and BIDS

https://github.com/carpentries-incubator/sdc-bids-intromri

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary

Keywords

alpha bids binder carpentries-incubator english helpwanted-list lesson mri neuroimaging python

Keywords from Contributors

beta carpentries-lab life-sciences metagenomics stable diffusion-mri
Last synced: 6 months ago · JSON representation ·

Repository

Introduction to MRI and BIDS

Basic Info
Statistics
  • Stars: 26
  • Watchers: 8
  • Forks: 19
  • Open Issues: 9
  • Releases: 3
Topics
alpha bids binder carpentries-incubator english helpwanted-list lesson mri neuroimaging python
Created over 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Authors

README.md

Introduction to Working with MRI Data in Python

Create a Slack Account with us Slack Status Binder

An introduction to working with magnetic resonance imaging (MRI) data in Python.

About the Lesson

This lesson teaches:

  • a (re?) introduction to MR nomenclature - with BIDS
  • how neuroimaging data is stored
  • "converting" your data to BIDS
  • BIDS apps
  • queueing up neuroimaging pipelines

Episodes

| # | Episode | Time | Question(s) | | --: | :------ | :--: | :------------------------------------------------------------------------- | | 1 | Before we start | 30 | What is Python and why should I learn it? | | 2 | From the scanner to our computer | 30 | What are the main MRI modalities?
What's the first step necessary to start working with MRI data? | | 3 | Anatomy of a NIfTI | 25 | How are MRI data represented digitally? | | 4 | Data organization with BIDS | 45 | | | 5 | Exploring open MRI datasets | 45 | How does standardizing neuroimaging data ease the data exploration process | | 6 | BIDS derivatives | 45 | |

Contributing

We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.

We'd like to ask you to familiarize yourself with our Contribution Guide and have a look at the more detailed guidelines on proper formatting, ways to render the lesson locally, and even how to write new episodes.

Please see the current list of issues for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter Contributing to a Project in Pro Git by Scott Chacon. Look for the tag good\_first\_issue. This indicates that the maintainers will welcome a pull request fixing this issue.

Maintainer(s)

Current maintainers of this lesson are

Authors

A list of contributors to the lesson can be found in AUTHORS

License

Instructional material from this lesson is made available under the Creative Commons Attribution (CC BY 4.0) license. Except where otherwise noted, example programs and software included as part of this lesson are made available under the MIT license. For more information, see LICENSE.

Citation

To cite this lesson, please consult with CITATION

Owner

  • Name: carpentries-incubator
  • Login: carpentries-incubator
  • Kind: organization

Citation (CITATION) 

Please cite as:

Michael Joseph, Jerrold Jeyachandra, and Erin Dickie (eds):
"Data Carpentry: Introduction to MRI Data Analysis." Version 2019.11, November 2019,
https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 9
  • Push event: 50
  • Pull request review event: 2
  • Pull request event: 12
  • Fork event: 1
  • Create event: 5
Last Year
  • Issues event: 1
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 9
  • Push event: 50
  • Pull request review event: 2
  • Pull request event: 12
  • Fork event: 1
  • Create event: 5

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 101
  • Total Committers: 8
  • Avg Commits per committer: 12.625
  • Development Distribution Score (DDS): 0.356
Past Year
  • Commits: 12
  • Committers: 2
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.083
Top Committers
Name Email Commits
Michael Joseph j****2@g****m 65
Jon Haitz Legarreta Gorroño j****a@g****m 20
Toby Hodges t****s@g****m 5
Erin W Dickie e****e 5
Annajiat Alim Rasel a****t@g****m 2
tigrlab-bot t****h@g****m 2
abbynoyce 6****e 1
Candace Makeda Moore, MD 3****e 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 14
  • Total pull requests: 40
  • Average time to close issues: 3 months
  • Average time to close pull requests: 19 days
  • Total issue authors: 7
  • Total pull request authors: 9
  • Average comments per issue: 0.71
  • Average comments per pull request: 1.03
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.43
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • josephmje (5)
  • jhlegarreta (3)
  • edickie (2)
  • ostanley (1)
  • travis-jeans (1)
  • drcandacemakedamoore (1)
  • carpentries-bot (1)
Pull Request Authors
  • josephmje (18)
  • jhlegarreta (16)
  • carpentries-bot (9)
  • annajiat (3)
  • drcandacemakedamoore (2)
  • Talishask (2)
  • zkamvar (1)
  • abbynoyce (1)
  • edickie (1)
Top Labels
Issue Labels
help wanted (5) good first issue (3) type:discussion (2) type:template and tools (1) type:instructor guide (1) type:enhancement (1) type: template and tools (1)
Pull Request Labels
type: template and tools (9)

Dependencies

.github/workflows/notebook.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
.github/workflows/pr-close-signal.yaml actions
  • actions/upload-artifact v3 composite
.github/workflows/pr-comment.yaml actions
  • actions/checkout v3 composite
  • carpentries/actions/check-valid-pr main composite
  • carpentries/actions/comment-diff main composite
  • carpentries/actions/download-workflow-artifact main composite
.github/workflows/pr-post-remove-branch.yaml actions
  • carpentries/actions/download-workflow-artifact main composite
  • carpentries/actions/remove-branch main composite
.github/workflows/pr-preflight.yaml actions
  • carpentries/actions/check-valid-pr main composite
  • carpentries/actions/comment-diff main composite
.github/workflows/pr-receive.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • carpentries/actions/check-valid-pr main composite
  • carpentries/actions/setup-lesson-deps main composite
  • carpentries/actions/setup-sandpaper main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/sandpaper-main.yaml actions
  • actions/checkout v3 composite
  • carpentries/actions/setup-lesson-deps main composite
  • carpentries/actions/setup-sandpaper main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/update-cache.yaml actions
  • actions/checkout v3 composite
  • carpentries/actions/check-valid-credentials main composite
  • carpentries/actions/update-lockfile main composite
  • carpentries/create-pull-request main composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/update-workflows.yaml actions
  • actions/checkout v3 composite
  • carpentries/actions/check-valid-credentials main composite
  • carpentries/actions/update-workflows main composite
  • carpentries/create-pull-request main composite
requirements.txt pypi
  • datalad *
  • matplotlib *
  • nibabel *
  • nilearn *
  • numpy *
  • pandas *
  • pybids *
binder/environment.yml pypi
  • dcm2bids *
  • pybids *