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kitchell / app-wmMask

This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.
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anatomy-preprocessing

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Abcdspec-compliant Run on Brainlife.io

app-wmMask

This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's parcellation.

Author

Funding

NSF-BCS-1734853 NSF-BCS-1636893

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/5a28180e67007b77e4d51cce# 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.
{
    "wm": ../wm.nii.gz
}
  1. Execute the main.m file via matlab

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 the white matter mask.

Dependencies

This App require matlab to run.