AtlasReader

AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images - Published in JOSS (2019)

https://github.com/miykael/atlasreader

Keywords from Contributors

bids brain-imaging fmri neuroimaging mesh

Scientific Fields

Medicine Life Sciences - 84% confidence

Artificial Intelligence and Machine Learning Computer Science - 83% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Python interface for generating coordinate tables and region labels from statistical MRI images

Basic Info

Host: GitHub
Owner: miykael
License: bsd-3-clause
Language: Jupyter Notebook
Default Branch: master
Homepage:
Size: 34.1 MB

Statistics

Stars: 106
Watchers: 8
Forks: 35
Open Issues: 13
Releases: 5

Created about 8 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

AtlasReader

This package provides a Python interface for generating coordinate tables and region labels from statistical MRI images. It is intended for neuroscience researchers and neuroimaging enthusiasts who are looking for a quick and easy way to localize and extract relevant peak and cluster information and create informative and nice looking overview figures.

Please check out our interactive notebook on mybinder.org to see atlasreader in action:

If you are using atlasreader in your publication, please cite the following paper:

Notter M. P., Gale D., Herholz P., Markello R. D., Notter-Bielser M.-L., & Whitaker K. (2019). AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images. Journal of Open Source Software, 4(34), 1257, https://doi.org/10.21105/joss.01257.

Installation

This package requires Python >= 3.6. Provided you have pip at your disposal, installing atlasreader is as simple as this:

bash pip install atlasreader

If you want to build atlasreader directly from source code, use the following code:

bash git clone https://github.com/miykael/atlasreader.git cd atlasreader python setup.py install

Usage

AtlasReader can either be run through the command line interface or directly within Python. The commands to do so are rather straight forward. Let's say you want to apply AtlasReader to a statistical image called file_name = 'stat_img.nii', and only want to keep clusters if they have more than 5 voxels:

Python

python from atlasreader import create_output create_output(file_name, cluster_extent=5)

Command Line

bash atlasreader file_name 5

Outputs

After executing AtlasReader on a given image, four kinds of outputs are generated:

An overview figure that shows the results within the whole brain at once
For each cluster, an informative figure showing the sagittal, coronal and transversal plane centered on the main peak of the cluster
A csv file containing relevant information about the peak of each cluster. This table contains the cluster association and location of each peak, its signal value at this location, the cluster extent (in mm, not in number of voxels), as well as the membership of each peak, given a particular atlas.
A csv file containing relevant information about each cluster. Table showing relevant information for the cluster extent of each ROI. This table contains the cluster association and location of each peak, the mean value within the cluster, the cluster extent (in mm, not in number of voxels), as well as the membership of each cluster, given a particular atlas.

Additional parameters

atlasreader.create_output has many additional parameters that allow you to change the way the clusters are generated and what kind of outputs are generated:

filename: Niimg_like A 3D statistical image.
cluster_extent: int Minimum number of contiguous voxels required to consider a cluster in filename
atlas: str or list, optional Name of atlas(es) to consider for cluster analysis. Default: 'default'
voxel_thresh: float, optional Threshold to apply to stat_img. Use direction to specify the directionality of the threshold. If a negative number is provided a percentile threshold is used instead, where the percentile is determined by the equation 100 - voxel_thresh. Default: 1.96
direction: str, optional Specifies the direction in which voxel_thresh should be applied. Possible values are 'both', 'pos' or 'neg'. Default: 'both'
prob_thresh: int, optional Probability (percentage) threshold to apply to atlas, if it is probabilistic. Default: 5
min_distance: float, optional Specifies the minimum distance (in mm) required between sub-peaks in a cluster. If None, sub-peaks will not be examined and only the primary cluster peak will be reported. Default: None
outdir: str or None, optional Path to desired output directory. If None, generated files will be saved to the same folder as filename. Default: None
glassplotkws: dict or None, optional Additional keyword arguments to pass to nilearn.plotting.plot_glass_brain. Default: None
statplotkws: dict or None, optional Additional keyword arguments to pass to nilearn.plotting.plot_stat_map. Default: None

For a more detailed explanation about the toolbox and the effect of the parameters above, see the example notebook. You can checkout the notebook either interactively via mybinder.org or explore a read-only version on nbviewer.jupyter.org.

How to get involved

We're thrilled to welcome new contributors!

If you're interested in getting involved, you should start by reading our contributing guidelines.

Once you're done with that, you can take a look at our list of active issues and let us know if there's something you'd like to begin working on.

If you've found a bug, are experiencing a problem, or have a question, create a new issue with some information about it!

Licence

AtlasReader is licensed under the BSD-3 license; however, the atlases it uses are separately licensed under more restrictive frameworks. By using AtlasReader, you agree to abide by the license terms of the individual atlases. Information on these terms can be found online at: https://github.com/miykael/atlasreader/tree/master/atlasreader/data

Owner

Name: Michael Notter
Login: miykael
Kind: user
Location: Lausanne, Switzerland

Twitter: miyka_el
Repositories: 49
Profile: https://github.com/miykael

Senior ML researcher & neuroscientist fascinated by hidden patterns, innovating in neuroimaging, computer vision, AR/VR, vital signs & multi-sensor sensing.

JOSS Publication

AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images

Published

February 24, 2019

DOI

10.21105/joss.01257

Volume 4, Issue 34, Page 1257

Authors

Michael Philipp Notter

The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland

Dan Gale

Centre for Neuroscience Studies, Queen's University, Kingston, Canada

Peer Herholz

Laboratory for Multimodal Neuroimaging, Philipps-University Marburg, Hesse, Germany, International Laboratory for Brain, Music and Sound Research, Université de Montréal & McGill University, Montréal, Canada, McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada

Ross Markello

McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada

Marie-Laure Notter-Bielser

Centre Leenaards de la Mémoire, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

Kirstie Whitaker

Alan Turing Institute, London, UK; Department of Psychiatry, University of Cambridge, Cambridge, UK

Editor

Christopher R. Madan

Citation (CITATION.cff)

# https://citation-file-format.github.io/
# https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
cff-version: 1.2.0

title: atlasreader

abstract: |
    A Python package to generate coordinate tables, region labels,
    and informative figures from statistical MRI images

message: If you use this software, please cite it as below.

repository-code: https://github.com/miykael/atlasreader

contact:
  - given-names: Michael Philipp
    family-names: Notter
    orcid: https://orcid.org/0000-0002-5866-047X
    affiliation: The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerlan

license: BSD-3-Clause

keywords:
  -  neuroimaging
  -  visualization

authors:
  - given-names: Michael Philipp
    family-names: Notter
    orcid: https://orcid.org/0000-0002-5866-047X
    affiliation: The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerlan

  - given-names: Dan
    family-names: Gale
    affiliation: "Centre for Neuroscience Studies, Queen's University, Kingston, Canada"
    orcid: https://orcid.org/0000-0002-9082-1659

  - given-names: Peer
    family-names:  Herholz
    affiliation: "Laboratory for Multimodal Neuroimaging, Philipps-University Marburg, Hesse, Germany; International Laboratory for Brain, Music and Sound Research, Université de Montréal & McGill University, Montréal, Canada; McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada"
    orcid: https://orcid.org/0000-0002-9840-6257

  - given-names: Ross
    family-names: Markello
    affiliation: "McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada"
    orcid: https://orcid.org/0000-0003-1057-1336

  - given-names: Marie-Laure
    family-names: Notter-Bielser
    affiliation: "Centre Leenaards de la Mémoire, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland"
    orcid: https://orcid.org/0000-0001-5507-4304

  - given-names: Anna
    family-names: Doll
    affiliation: "Department of Psychology, University of Bielefeld, Bielefeld, Germany."
    orcid: https://orcid.org/0000-0002-0799-0831

  - given-names: Rémi
    family-names: Gau
    website: https://github.com/Remi-Gau
    affiliation: Origami lab, McGill University, Montréal, Canada
    orcid: https://orcid.org/0000-0002-1535-9767

  - given-names: Kirstie
    family-names: Whitaker
    affiliation: "Alan Turing Institute, London, UK; Department of Psychiatry, University of Cambridge, Cambridge, UK"
    orcid: https://orcid.org/0000-0001-8498-4059

GitHub Events

Total

Issues event: 3
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Issue comment event: 6
Push event: 18
Pull request event: 4
Fork event: 4

Last Year

Issues event: 3
Watch event: 15
Issue comment event: 6
Push event: 18
Pull request event: 4
Fork event: 4

Committers

Last synced: 5 months ago

All Time

Total Commits: 286
Total Committers: 10
Avg Commits per committer: 28.6
Development Distribution Score (DDS): 0.493

Past Year

Commits: 7
Committers: 4
Avg Commits per committer: 1.75
Development Distribution Score (DDS): 0.571

Top Committers

Name	Email	Commits
miykael	m**r@h**m	145
Ross Markello	r**o@g**m	45
Remi Gau	r**u@h**m	40
Dan Gale	d**e@g**m	27
M.Notter	m**r@a**m	11
Kirstie Whitaker	k**1@c**k	10
AnnaD	4****5	3
dependabot[bot]	4****]	3
Peer Herholz	h**r@g**m	1
Federico Mengozzi	1****o	1

Committer Domains (Top 20 + Academic)

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Issues and Pull Requests

Last synced: 4 months ago

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Total issues: 62
Total pull requests: 77
Average time to close issues: 2 months
Average time to close pull requests: 23 days
Total issue authors: 22
Total pull request authors: 9
Average comments per issue: 3.37
Average comments per pull request: 2.4
Merged pull requests: 71
Bot issues: 0
Bot pull requests: 20

Past Year

Issues: 3
Pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: 14 days
Issue authors: 3
Pull request authors: 3
Average comments per issue: 0.33
Average comments per pull request: 0.8
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 1

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miykael (22)
andrewheusser (12)
Remi-Gau (5)
danjgale (2)
AdelleBernal (2)
andreifoldes (2)
rmarkello (2)
tilsley-p (1)
ElijahMak (1)
saigerutherford (1)
AtomicNess123 (1)
mriedel56 (1)
const7 (1)
nm9404 (1)
HuygelierH (1)

Pull Request Authors

miykael (28)
github-actions[bot] (13)
rmarkello (13)
dependabot[bot] (9)
Remi-Gau (7)
danjgale (4)
AnnaD15 (2)
fedemengo (2)
PeerHerholz (1)

Top Labels

Issue Labels

help wanted (6) enhancement (6) bug (5) question (4) good first issue (3) testing (2)

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dependencies (9)

Packages

Total packages: 1
Total downloads:
- pypi 150 last-month
Total docker downloads: 10

Total dependent packages: 1
Total dependent repositories: 2
Total versions: 8
Total maintainers: 1

pypi.org: atlasreader

A toolbox for generating cluster reports from statistical maps

Homepage: http://github.com/miykael/atlasreader
Documentation: https://atlasreader.readthedocs.io/
License: BSD-3-Clause
Latest release: 0.3.2
published almost 2 years ago

Versions: 8
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 150 Last month
Docker Downloads: 10

Rankings

Docker downloads count: 4.1%

Dependent packages count: 4.8%

Forks count: 7.1%

Stargazers count: 7.8%

Average: 8.7%

Dependent repos count: 11.6%

Downloads: 16.7%

Maintainers (1)

mnotter

Last synced: 4 months ago

AtlasReader

Science Score: 100.0%

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

AtlasReader

Installation

Usage

Python

Command Line

Outputs

Additional parameters

How to get involved

Licence

Owner

JOSS Publication

AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

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Committer Domains (Top 20 + Academic)

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pypi.org: atlasreader

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