giulia-berto/app-ants-CFA-registration

CFA-based non linear ANTs registration of the tensor to the FMRIB58_FA_1mm.nii.gz template or the IITmean_FA template.

app-template-python

This is a template for a python-based brainlife.io/app

app-example-documentation

This is an example of how to write documentation (readme.md and license.md for Apps on brainlife.io)

Write the following here...

1. What the App does, and how it does it at the basic level.
2. Briefly explain what 1) means for novice users in a language that 1st year psychology student can understand it.
3. Briefly description of input / output files.

Authors

• Franco Pestilli

Contributors

• Franco Pestilli

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

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 code and publications. Copy and past the following lines into your repository when using this code.

Citations

We ask that you the following articles when publishing papers that used data, code or other resources created by the brainlife.io community.

1. 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/bl.app.444 via the "Execute" tab.

Running Locally (on your machine)

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"
}

3. Launch the App by executing main

./main

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5a0f0fad2c214c9ba8624376#5a050966eec2b300611abff2 && mv 5a0f0fad2c214c9ba8624376#5a050966eec2b300611abff2 .

Output

All output file (a resampled T1w NIFTI-1 file) will be generated inside the current working directory (pwd), inside a specifc directory called:

out_dir

Dependencies

This App only requires DIPY.org to run.