This service runs mrtrix tracking using SD_PROB, SD_STREAM, and DT_STREAM algorithms. It generates 3 separate track output for each algorithms.
- Brent McPherson (bcmcpher@iu.edu)
- Lindsey Kitchell (kitchell@iu.edu)
- Soichi Hayashi (hayashis@iu.edu)
- Franco Pestilli (franpest@indiana.edu)
You can submit this App online at ..
- For dtiinit input https://doi.org/10.25663/bl.app.59
- For dwi input https://doi.org/10.25663/bl.app.105
via the "Execute" tab.
- git clone this repo.
- Inside the cloned directory, create
config.json
with something like the following content with paths to your input files.
{
"dwi": "/path/to/dwi/dwi.nii.gz",
"bvals": "/path/to/dwi/dwi.bvals",
"bvecs": "/path/to/dwi/dwi.bvecs",
"freesurfer": "/path/to/freesurfer/output",
"fibers": 500000,
"fibers_max": 1000000
}
- Launch the App by executing
main
./main
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 5a050a00eec2b300611abff3 && mv 5a050a00eec2b300611abff3 input/dwi
bl dataset download 5a065cc75ab38300be518f51 && mv 5a065cc75ab38300be518f51 input/freesurfer
All output files will be generated under the current working directory (pwd). The main output of this App is a file called output.mat
. This file contains following object.
ADD
output.XXX
contains XXX.
The secondary output of this app is product.json
. This file allows web interfaces, DB and API calls on the results of the processing.
This App only requires singularity to run. If you don't have singularity, you will need to install following dependencies.