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CPP ROI

⚠️ ⚠️ ⚠️

This code is fairly unstable (:boom:) and might still change a lot.

Also this code currently has 0% test coverage...

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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

% Th 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 intitialized when running initCppSpm.

Dependencies

======= TODO

Dependencies	Used version
Matlab	20???
or octave	4.?
SPM12	v7487

• bids-matlab (INSERT URL)

• currently still needs some CPP_SPM function but ultimately should be standalone: this will most likely happen when some functions are passed to bids-matlab

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

Features

• create ROI from probability maps
• create ROI filenames that "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 probabilty maps
  • the probabilistic maps of visual topography in human cortex:
    • https://scholar.princeton.edu/napl/resources
    • Wang, L., Mruczek, R. E., Arcaro, M. J., & Kastner, S. (2015). Probabilistic Maps of Visual Topography in Human Cortex. Cerebral cortex (New York, N.Y. : 1991), 25(10), 3911–3931. https://doi.org/10.1093/cercor/bhu277

Also includes:

• Yeo's 7 networks "atlas"
  • add REF and URL

Contributing

Contributors