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.

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

Fire up Octave or Matlab and type

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 CPP_SPM, you got nothing to do as CPP_ROI 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”

Marco Barilari 💻 📖 🤔	Remi Gau 💻 📖 🚇 🎨 👀 🐛 ⚠️	Jeanne Caron-Guyon 🤔 📓	Iqra Shahzad 📓	Federica Falagiarda 🐛 📓	Ceren Battal 💻 👀 📓	Jacek Matuszewski 🐛 📓
Ying Yang 🐛 📓