This app will fit the NODDI model (Zhang et al, 2012) using the original matlab package.
- Brad Caron (bacaron@utexas.edu)
- Soichi Hayashi (shayashi@iu.edu)
brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your publications and code reusing this code.
We kindly ask that you cite the following articles when publishing papers and code using this code.
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Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). https://doi.org/10.1038/s41597-019-0073-y
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Zhang H, Schneider T, Wheeler-Kingshott CA, Alexander DC. NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain. Neuroimage. 2012 Jul 16;61(4):1000-16. doi: 10.1016/j.neuroimage.2012.03.072. Epub 2012 Mar 30. PMID: 22484410.
You can submit this App online at https://doi.org/10.25663/brainlife.app.158 via the 'Execute' tab.
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git clone this repo
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Inside the cloned directory, create
config.jsonwith something like the following content with paths to your input files.
{
"dwi": "/input/dwi/dwi.nii.gz",
"bvecs": "/input/dwi/bvecs.nii.gz",
"bvals": "/input/dwi/bvals.nii.gz",
"mask": "/input/brainmask/mask.nii.gz"
}You can download sample datasets from Brainlife using Brainlife CLI.
npm install -g brainlife
bl login
mkdir input
bl dataset download
- Launch the App by executing 'main'
./mainThe main output of this App is a NODDI datatype, containing the volume maps for neurite density index (ndi), orientation dispersion index (odi) and isotropic volume fraction (isovf).
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.