Paolopost / app-tracking

This service runs mrtrix 2.0 tracking spanning over multiple tracking methods and parameters (Probabilistic and Deterministic tracking). It generates three separate tracking outputs for each algorithm.

app-tracking

This service runs mrtrix tracking using SD_PROB, SD_STREAM, and DT_STREAM algorithms. It generates 3 separate track output for each algorithms.

Authors

• Brent McPherson ([e-mail])
• Lindsey Kitchell ([e-mail])
• Soichi Hayashi ([e-mail])

Project director

• Franco Pestilli ([e-mail])

Funding

Running the App

On Brainlife.io

You can submit this App online at ..

• For dtiinit input https://doi.org/10.25663/bl.app.59
• For dwi input https://doi.org/10.25663/bl.app.105

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.

{
    "dwi":  "/path/to/dwi/dwi.nii.gz",
    "bvals":  "/path/to/dwi/dwi.bvals",
    "bvecs":  "/path/to/dwi/dwi.bvecs",
    "freesurfer": "/path/to/freesurfer/output",
    "fibers": 500000,
    "fibers_max": 1000000
}

3. Launch the App by executing main

./main

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5a050a00eec2b300611abff3 && mv 5a050a00eec2b300611abff3 input/dwi
bl dataset download 5a065cc75ab38300be518f51 && mv 5a065cc75ab38300be518f51 input/freesurfer

Output

All output files will be generated under the current working directory (pwd). The main output of this App is a file called output.mat. This file contains following object.

ADD

output.XXX contains XXX.

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 only requires singularity to run. If you don't have singularity, you will need to install following dependencies.

• Matlab: https://www.mathworks.com/products/matlab.html
• jsonlab: https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files
• VISTASOFT: https://github.com/vistalab/vistasoft/
• MRTRIX 2.0: https://jdtournier.github.io/mrtrix-0.2/index.html