This code is fairly unstable and might still change.
So make sure you "pin" which version or commit you are using for a given project, if you don't want your code to break in the future.
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:
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.gitFire 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.
======= 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
libfolder.
- 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
- 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"