svincibo/app-fsltopupeddy

This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.

app-FSLTopupEddy

This app will correct for phase-encoding, eddy current, and motion artifacts in DWI images using FSL's Top-up and Eddy functions. Inputs are reverse-phase encoded DWI images (x2), and the outputs are a corrected DWI datatype and a brainmask datatype.

Authors

• Brad Caron ([email protected])

Contributors

• Soichi Hayashi ([email protected])
• Franco Pestilli ([email protected])
• Brent McPherson ([email protected])

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.155 via the "Execute" tab.

Running Locally (on your machine)

1. git clone this repo.
2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
        "diff": "./input/dwi1/dwi.nii.gz",
        "bval": "./input/dwi1/dwi.bvals",
        "bvec": "./input/dwi1/dwi.bvecs",
        "rdif": "./input/dwi2/dwi.nii.gz",
        "rbvc": "./input/dwi2/dwi.bvecs",
        "rbvl": "./input/dwi2/dwi.bvals",
        "param":  0.00006999,
        "encode": "PA"
}

Sample Datasets

You can download sample datasets from Brainlife using Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5b96bbf2059cf900271924f3 && mv 5b96bbf2059cf900271924f3 input/dwi1
bl dataset download 5b96bbf2059cf900271924f3 && mv 5b96bbf2059cf900271924f3 input/dwi2

3. Launch the App by executing main

./main

Output

The main output of this App is DWI datatype and a mask datatype.

Product.json

The secondary output of this app is product.json. This file allows web interfaces, DB and API calls on the results of the processing.

Dependencies

This App requires the following libraries when run locally.

• singularity: https://singularity.lbl.gov/
• FSL: https://hub.docker.com/r/brainlife/fsl/tags/5.0.9
• jsonlab: https://github.com/fangq/jsonlab.git