sraashis / coinstac_ddfnc_pipeline

test repo to demonstrate ddfnc and group ica pipelines

Coinstac Group ICA/ddFNC Pipeline

This repository compiles submodules utilized for Group ICA and ddFNC.

The ddFNC pipeline consists of two distinct parts - Group or Spatially Constrained ICA first, followed by ddFNC.

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 https://github.com/MRN-Code/coinstac_ddfnc_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/ ;
cp test/remote/simulatorRun/NeuroMark.nii test/local0/simulatorRun/ ;
cp test/remote/simulatorRun/NeuroMark.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 ddfnc .
sudo coinstac-simulator

Spatially Constrained ICA

The stages of Spatially Constrained ICA are

• local spatially constrained ICA (performed with GIFT)

Group ICA

The stages of Group ICA are:

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

ddFNC

The stages of ddFNC are:

• Group/ScICA ICA (as given above)
• Local post-processing of timecourses (including windowing)
• Decentralized Clustering