app-extract-peaks

This App extracts the peaks of a spherical harmonic function at each voxel using the MRtrix command sh2peaks. This code is part of the TractSeg package developed by (Wasserthal et al., 2018), under Apache-2.0 License: https://github.com/MIC-DKFZ/TractSeg.

Authors

Giulia Bertò

Funding Acknowledgement

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.

Citations

We kindly ask that you cite the following articles when publishing papers and code using this code.

Tournier, J.‐D., Calamante, F. and Connelly, A. (2012), MRtrix: Diffusion tractography in crossing fiber regions. Int. J. Imaging Syst. Technol., 22: 53-66. https://doi.org/10.1002/ima.22005
TractSeg - Fast and accurate white matter tract segmentation (free arxiv version) [NeuroImage 2018]
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

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.172 via the “Execute” tab.

Inputs:
Mandatory inputs are (i) the dwi data (multi-shell and not nomalized) and (ii) the T1 anatomical image. Optionally, you can provide also the brain mask (if not provided, it will be computed using the BET command from FSL).

Output:
The CSD peaks.

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.

{
        "dwi": "./input/dwi/dwi.nii.gz",
	"bvecs": "./input/bvecs/dwi.bvecs",
	"bvals": "./input/bvals/dwi.bvals",
	"t1": "./input/t1.nii.gz",
	"mask": "./input/mask.nii.gz",
	"csd": "csd_msmt_5tt"
}

Launch the App by executing main

./main

Output

The main output of this App is a file called peaks.nii.gz, which is a 4D nifti image containing the peaks of a spherical harmonic function at each voxel (from sh2peaks).

Dependencies

This App only requires singularity to run.

giulia-berto/app-extract-peaks