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cpp_roi

Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets. Mostly volume-based and SPM centric.

https://github.com/cpp-lln-lab/cpp_roi

Science Score: 67.0%

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    Low similarity (14.8%) to scientific vocabulary

Keywords

bids mri roi spm12
Last synced: 6 months ago · JSON representation ·

Repository

Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets. Mostly volume-based and SPM centric.

Basic Info
Statistics
  • Stars: 5
  • Watchers: 5
  • Forks: 6
  • Open Issues: 11
  • Releases: 5
Topics
bids mri roi spm12
Created almost 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

pre-commit.ci status miss hit tests and coverage with matlab codecov All Contributors DOI

CPP ROI

Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets.

Mostly volume-based and SPM centric.

For surface based and freesurfer ROIs see for example:

  • https://github.com/noahbenson/neuropythy

Installation

Download this repository and unzip the content where you want to install it.

Or clone the repo.

bash git clone https://github.com/cpp-lln-lab/CPP_ROI.git

Fire up Octave or Matlab and type

```matlab cd CPP_ROI

% The following adds the relevant folders to your path. % This needs to be done once per session (your path will not be saved)

initCppRoi ```

If you are using CPPSPM, you got nothing to do as CPPROI is already installed as a submodule, and initialized when running initCppSpm.

Dependencies

| Dependencies | Used version | | --------------------------------------------------------------- | ------------ | | Matlab | 20??? | | or octave | 4.? | | SPM12 | v7487 | | bids-matlab | >=0.1.0 |

  • Other dependencies (MarsBar) are shipped with CPP_ROI in the lib folder.

Features

  • create ROI from probability maps
  • create ROI from atlas (see below)
  • create ROI filenames that are "BIDS-ish"
  • extract ROI with a given numerical label
  • extract ROI from one hemisphere
  • breaks a cluster image into several ROIs with each their own label

Atlas

  • Can help generate ROI based on:
    • the SPM Anatomy toolbox (INSERT URL)
    • the SPM neuromorphometric atlas
    • neurosynth probability maps
    • A multi-modal parcellation of human cerebral cortex [@glasser2016]
    • the probabilistic maps of visual topography in human cortex [@wang2014]
      • https://scholar.princeton.edu/napl/resources
    • the probabilistic functional atlas of human occipito-temporal visual cortex [@rosenke2020]
    • extended Human Connectome Project multimodal parcellation atlas of the human cortex and subcortical areas [@huang2022]

Also includes:

  • Yeo's 7 networks "atlas" <!-- add REF and URL -->
Marco Barilari
Marco Barilari
 Remi Gau
Remi Gau
 Jeanne Caron-Guyon
Jeanne Caron-Guyon
Iqra Shahzad
Iqra Shahzad
 Federica Falagiarda
Federica Falagiarda
 Ceren Battal
Ceren Battal
 Jacek Matuszewski
Jacek Matuszewski
Ying Yang
Ying Yang

Owner

  • Name: Crossmodal Perception and Plasticity laboratory
  • Login: cpp-lln-lab
  • Kind: organization
  • Location: Louvain la Neuve, Belgium

Citation (CITATION.cff) 

cff-version: 1.2.0

title: "CPP ROI"

version: 0.4.0

abstract: Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets.

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

repository-code: "https://github.com/cpp-lln-lab/CPP_ROI"

contact:
  - affiliation: "Université catholique de Louvain"
    email: remi.gau@uclouvain.be
    family-names: Gau
    given-names: Rémi

authors:
- family-names: "Gau"
  given-names: "Rémi"
  orcid: "https://orcid.org/0000-0002-1535-9767"
  affiliation: "Université catholique de Louvain"

- family-names: "Barilari"
  given-names: "Marco"
  orcid: "https://orcid.org/0000-0002-3313-3120"
  affiliation: "Université catholique de Louvain"

- family-names: "Battal"
  given-names: "Ceren"
  orcid: "https://orcid.org/0000-0002-9844-7630"
  affiliation: "Université catholique de Louvain"

- family-names: "Falagiarda"
  given-names: "Federica"
  orcid: "https://orcid.org/0000-0001-7844-1605"
  affiliation: "Université catholique de Louvain"

- family-names: "Caron-Guyon"
  given-names: "Jeanne"
  orcid: "https://orcid.org/0000-0001-8681-5267"
  affiliation: "Université catholique de Louvain"

- family-names: "Yang"
  given-names: "Ying"
  orcid: "https://orcid.org/0000-0002-4157-2975"
  affiliation: "Université catholique de Louvain"

- family-names: "Matuszewski"
  given-names:  "Jacek"
  affiliation: "Université catholique de Louvain"
  orcid: "https://orcid.org/0000-0001-9752-3294"

license: GPL-3.0

keywords:
  - BIDS
  - brain imaging data structure
  - neuroimaging
  - MRI
  - MATLAB
  - Octave
  - SPM
  - ROI
  - region of interest

GitHub Events

Total
  • Delete event: 7
  • Issue comment event: 12
  • Push event: 8
  • Pull request review event: 7
  • Pull request event: 15
  • Create event: 8
Last Year
  • Delete event: 7
  • Issue comment event: 12
  • Push event: 8
  • Pull request review event: 7
  • Pull request event: 15
  • Create event: 8

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 12 days
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 1.13
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 0
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 12 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 1.13
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 7
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Top Authors
Issue Authors
  • marcobarilari (1)
Pull Request Authors
  • dependabot[bot] (16)
  • pre-commit-ci[bot] (5)
  • Remi-Gau (5)
  • allcontributors[bot] (2)
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dependencies (16) github_actions (14) submodules (2)

Dependencies

requirements.txt pypi
  • Sphinx *
  • miss_hit ==0.9.30
  • myst-parser *
  • pre-commit *
  • rstcheck *
  • sphinx-copybutton *
  • sphinx_rtd_theme *
  • sphinxcontrib-matlabdomain *
.github/workflows/run_tests_matlab.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • matlab-actions/run-command v1.1.2 composite
  • matlab-actions/setup-matlab v1.2.3 composite
.github/workflows/validate_cff.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite