app-crop_reorient_t1

This application will crop and reorient the T1 image to standard orientation and FOV.

Author

• Lindsey Kitchell ([email protected])

Funding

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/5a0f38bf31769f1e4d46cc58v 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 output of this App is the cropped/reoriented T1 image.

Dependencies

This App require FSL to run. FSL can be obtained from FSL.