app-warp-t1

This App applies the given non-linear warp to the T1 image and to all Diffusion Tensor Image Scalars. WARNING: all the given inputs should be in the same anatomical space.

Authors

• Giulia Bertò (giulia.berto.4@gmail.com)

Contributors

• Paolo Avesani (avesani@fbk.eu)

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.

1. Avants, B.B., Epstein, C.L., Grossman, M., Gee, J.C., 2008. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 12 (1), 26–41. doi: 10.1016/j.media.2007.06.004.

2. 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.448 via the “Execute” tab.

Input:
T1 image and Diffusion Tensor Image Scalars (tensor datatype) in the same anatomical space. Up to now, supported scalars are: FA (Fractional Anisotropy), MD (Mean Diffusivity), RD (Radial Diffusivity), and AD (Axial Diffusivity).

Output:
T1 image and Diffusion Tensor Image Scalars (tensor datatype) warped.

Running locally

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

{
   "t1":    "./t1.nii.gz",
   "fa":    "./tensor/fa.nii.gz",
   "md":    "./tensor/md.nii.gz",
   "rd":    "./tensor/rd.nii.gz",
   "ad":    "./tensor/ad.nii.gz",
} 

3. Launch the App by executing main.

./main

Output

The main outputs of this App are the T1 and the Diffusion Tensor Image Scalars (tensor datatype) warped with the given non-linear warp.

Dependencies

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

• ANTs >=2: https://github.com/ANTsX/ANTs

MIT Copyright (c) 2020 brainlife.io The University of Texas at Austin and Indiana University