app-freesurfer

This is a Brainlife wrapper for Freesurfer; a popular brain segmentation tool developed by Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital. This wrapper executes recon_all to generate various data products used by other Brainlife Apps.

Authors

Franco Pestilli (franpest@indiana.edu)
Lindsey Kitchell (kitchell@indiana.edu)

Contributors

Soichi Hayashi (hayashis@iu.edu)
Brent McPherson (bcmcpher@iu.edu)

Project director

Franco Pestilli (franpest@indiana.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.0 via the "Execute" tab.

Running Locally (on your machine)

git clone this repo.
Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
    "t1": "/input/t1/t1.nii.gz"
}

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 5a050966eec2b300611abff2 && mv 5a050966eec2b300611abff2 input/t1

Output

The main output of this App is a directory named output. It contains various freesurfer sub directories.

hayashis@xps15:~/Downloads/output $ ls -la
total 40
drwxr-xr-x 10 hayashis hayashis 4096 Nov 10  2017 .
drwx------  3 hayashis hayashis 4096 Sep 11 09:34 ..
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 label
drwxrwxr-x  4 hayashis hayashis 4096 Nov 10  2017 mri
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 scripts
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 stats
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 surf
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 tmp
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 touch
drwxrwxr-x  2 hayashis hayashis 4096 Nov 10  2017 trash

Dependencies

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

Freesurfer: https://surfer.nmr.mgh.harvard.edu/

giulia-berto/app-freesurfer