This App was deprecated by https://github.com/brain-life/app-acpcART

app-autoalignacpc

This App will align brains to the AC-PC plane by guessing their location given MNI coordinates using vistasoft from Stanford Vision Imaging Science and Technology Lab.

The algorithm will output t1.nii.gz containing voxel data that is aligned to AC-PC. The affine matrix will be reset to identity.

Authors

• Lindsey Kitchell (kitchell@indiana.edu)
• Soichi Hayashi (hayashis@iu.edu)

Project directors

• Franco Pestilli (franpest@indiana.edu)

Funding

Running the App

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": "./input/anat/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 5a050966eec2b300611abff2 && mv 5a050966eec2b300611abff2 input/anat

## Output

The `t1.nii.gz` will be generated in the current directory which contains AC-PC aligned version of the input `t1.nii.gz`. 

### Dependencies

This App only requires [singularity](https://www.sylabs.io/singularity/) to run. If you don't have singularity, you will need to install following dependencies.  

  - Matlab: https://www.mathworks.com/products/matlab.html
  - jsonlab: https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files
  - VISTASOFT: https://github.com/vistalab/vistasoft/