trendscenter / coinstac-mancova

MANCOVA analysis of covariates following backreconstruction

Coinstac Group ICA/dMANCOVA

This repository compiles submodules utilized for Group ICA and MANCOVA

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

Running in the Simulator

This pipeline has been tested with version 5.1.0 of the COINSTAC simulator

Install the simulator:

npm i -g coinstac-simulator

Download this repository

git clone https://github.com/trendscenter/coinstac-mancova.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

mkdir -p test/input/remote/simulatorRun ;
cp local_data/* test/input/remote/simulatorRun
cp local_data/* test/input/local0/simulatorRun
cp local_data/* test/input/local1/simulatorRun

Copy your NIfTI files and corresponding cavariates CSV files into the test site folders. The covariates.csv file should only have data for the NIfTI files in the corresponding site. Below is an example covariates.csv file.

age	diagnosis	filename
25.0	1.0	vsdwa_000123.nii.gz
42.0	0.0	vsdwa_000456.nii.gz

After those steps, the test folder should look similar to this (probably with different .nii.gz files).

test
├── input
│   ├── local0
│   │   └── simulatorRun
│   │       ├── NeuroMark.nii
│   │       ├── covariate_keys.csv
│   │       ├── covariates.csv
│   │       ├── mask.nii
│   │       ├── vsdwa_000123.nii.gz
│   │       ├── vsdwa_000456.nii.gz
│   ├── local1
│   │   └── simulatorRun
│   │       ├── NeuroMark.nii
│   │       ├── covariate_keys.csv
│   │       ├── covariates.csv
│   │       ├── mask.nii
│   │       ├── vsdwa_000789.nii.gz
│   │       ├── vsdwa_000800.nii.gz
│   └── remote
│       └── simulatorRun
│           ├── NeuroMark.nii
│           └── mask.nii
└── inputspec.json

Finally, run using the bash script (will require sudo unless your user is in the docker group)

bash run.sh

or

Run using the following commands

docker build  -t dmancova .
coinstac-simulator --silly

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 dMANCOVA are:

• ...

coinstac-mancova's Issues

Does not work for different filenames

Currently, the code doesn't work unless the CSV files are named covariates.csv and covariate_keys.csv. The answer might be to separate the CSV files into different variables on the UI. You can see in the code below that the CSV files seem to depend on order within a list, and I'm not sure how that order is established.

coinstac-mancova/coinstac_mancova/local.py

Line 73 in 441069a

covariate_file = os.path.join(state["baseDirectory"], csv_filename[0])

Need to version all the dependencies in requirements.txt

coinstac-mancova/requirements.txt

Line 11 in 441069a

h5py