app-generatetractmasks

This app generate binary masks of segmented fiber tracts

Author

• Lindsey Kitchell (kitchell@indiana.edu)
• Daniel Bullock (dnbulloc@iu.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/592dc03eb3cd7c00211dc239 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": ../ti.nii.gz,
    "afq_fg": afq_fgclassifiedoutput
}

3. Execute the main.m file via matlab or the main file via singularity

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.

Output

The output of this App is a folder with the nifti images of the binary track masks.

Dependencies

This App require matlab or singularity to run.