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.
- Franco Pestilli ([email protected])
- Lindsey Kitchell ([email protected])
- Soichi Hayashi ([email protected])
- Brent McPherson ([email protected])
- Franco Pestilli ([email protected])
You can submit this App online at https://doi.org/10.25663/bl.app.0 via the "Execute" tab.
- git clone this repo.
- Inside the cloned directory, create
config.jsonwith something like the following content with paths to your input files.
{
"t1": "/input/t1/t1.nii.gz"
}- Launch the App by executing
main
./mainIf 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
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
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/