Coinstac Group ICA Pipeline

This repository compiles submodules utilized for Group ICA, WITHOUT ddFNC as an option.

Running in the Simulator

This pipeline has been tested with the latest version of the COINSTAC simulator.

Install the simulator:

npm i -g coinstac-simulator

Download this repository

git clone [email protected]:trendscenter/coinstac_gica_pipeline.git

Initialize submodules

git submodule update --init --recursive

Copy the mask and template into the local input folders, using the bash script

bash copy_data.sh

or the following commands

cp test/remote/simulatorRun/mask.nii test/local0/simulatorRun/ ;
cp test/remote/simulatorRun/mask.nii test/local1/simulatorRun/ ;

Finally, run using the bash script (will require entry of password for sudo)

bash run.sh

or

Run using the following commands

sudo docker build  -t gica .
sudo coinstac-simulator

Spatially Constrained ICA

The stages of Spatially Constrained ICA are

• local spatially constrained ICA (performed with GIFT), coordinate with COINSTAC

Output:

• NIFTI files containing a set of independent spatial maps and a set of corresponding timecourses
• An HTML report providing visualizations of spatial maps, timecourses and spectra, static functional network connectivity, and kurtosis
• .mat files for each individual independent component
• NIFTI files containing average spatial maps over all local subjects

Group ICA

The stages of Group ICA are:

• decentralized row means
• decentralized PCA
• local ICA (either with Infomax ICA, spatially-constrained ICA, or other)

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Linked Repositories/Submodules

Briefly, there are a number of linked repositories attached to this pipeline:

• coinstac_backreconstruction: used for decentralized spatio-temporal regression and decentralized spatially constrained ICA as part of GIG-ICA
• coinstac_decentralized_pcA: