yoaman/app-ants-mni

ANTs transformation and tractogram registration in MNI space, using as the reference template the MNI152 T1 at 1.25 mm. WARNING: all the given inputs should be in the same anatomical space.

app-ants-mni

This App computes a non-linear registration of a .tck file in MNI space using the Advanced Normalization Tools (ANTs) algorithm. First, a non-linear warp is computed to register the T1 image to the template image, which is the MNI152 T1 at 1.25 mm. Then, the same transformation is applied to the .tck file. For this reason it is important that the T1 image and the .tck file (and the mask, if provided) are in the same anatomical space.

Authors

• Giulia Bertò ([email protected])

Contributors

• Paolo Avesani ([email protected])

Funding Acknowledgement

We kindly ask that you acknowledge the funding below in your publications and code reusing this code.

Citation

We kindly ask that you cite the following article 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.

Running the app

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.202 via the “Execute” tab.

Inputs:
A .tck file and a T1 image, in the same anatomical space. Optionally, you can provide also a brain mask, in the same anatomical space. If the mask is not provided, the Brain Extraction Tool (BET) algorithm will be used for brain extraction.

Outputs:
This App produces 3 outputs. The main output of this App is (i) the .tck file in MNI space. Other outputs are (ii) the warp and the inverse-warp used for the registration, and (iii) the T1 in MNI space.

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:

{
    "track": "./track.tck",
    "t1": "./t1.nii.gz",
    "mask": "./mask.nii.gz"
}

3. Launch the App by executing main.

./main

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
• FSL >=5: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
• MRtrix >=3: https://www.mrtrix.org/

MIT Copyright (c) 2020 Bruno Kessler Foundation (FBK)