app-biafieldcorrection

This service corrects the bias field of T1 and DWI images using ANTs

Author

• Lindsey Kitchell (kitchell@indiana.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/5a0f2dba19b13d1e190f1eeb# and https://brainlife.io/app/5ae9c55df446980028b15eba# 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
}

3. Execute the main file via command line

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 main output of this App is the bias corrected image (t1 or dwi) and the bia.nii.gz field image.

Dependencies

This App require ANTs to run. ANTs can be obtained from http://stnava.github.io/ANTs/.