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.
- Giulia Bertò (giulia.berto.4@gmail.com)
- Paolo Avesani (avesani@fbk.eu)
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.
-
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.
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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
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.
- git clone this repo.
- 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",
}
- Launch the App by executing
main
.
./main
The main outputs of this App are the T1 and the Diffusion Tensor Image Scalars (tensor datatype) warped with the given non-linear warp.
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