app-vistasoft-registration

This app will register a DWI image to a T1w image and rotate the bvecs. First, a brainmask is created of from the DWI image using FSL's bet function by running the brainmask script. Then, the brainmask image is aligned to the T1 using Vistasoft's dtiRawAlignToT1 function. The transformation matrix from this is then used to resample the DWI image using Vistasoft's dtiRawResample function. Finally, the bvecs are rotated based on the transformation using Vistasoft's dtiRawReorientBvecs function. These last three steps are all performed by running the main script.

Authors

• Brad Caron ([email protected])

Contributors

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

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.50 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.

{
        "t1": "./input/t1/t1.nii.gz",
        "dwi": "./input/dwi/dwi.nii.gz",
        "bvals": "./input/dwi/dwi.bvals",
        "bvecs": "./input/dwi/dwi.bvecs",
        "interpolation": "linear"
}

Sample Datasets

You can download sample datasets from Brainlife using Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5b96bbbf059cf900271924f2 && mv 5b96bbbf059cf900271924f2 input/t1
bl dataset download 5b96bbf2059cf900271924f3 && mv 5b96bbf2059cf900271924f3 input/dwi

3. Launch the App by executing main

./main

Output

The main output of this App is a dwi.nii.gz, along with the bvals and bvecs. These can then be used in any app requiring a dwi file.

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/
• VISTASOFT: https://github.com/vistalab/vistasoft/
• SPM 8: https://www.fil.ion.ucl.ac.uk/spm/software/spm8/
• FSL: https://hub.docker.com/r/brainlife/fsl/tags/5.0.9
• jsonlab: https://github.com/fangq/jsonlab.git