app-plotAFQ

This App plots the fibers outputted from app-tractclassification.

Author

• Lindsey Kitchell (kitchell@indiana.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/5967b45e81d7ef0021538e89 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.

{
    "coronal": 85,
    "sagittal": 74,
    "axial": 48,
    "AFQ": "testdata/track/tracts",
    "t1": "testdata/anat/t1.nii.gz",
    "img_max": 2,
    "img_min": -0.5
}

If you have singlarity install on your local machine:

3. Launch the App by executing 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.

Output

The output of this app will be a folder with images of the AFQ tracts.

Dependencies

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

RUN apt-get update && apt-get install -y python-pip
RUN apt-get install -y xvfb x11-xkb-utils
RUN apt-get install -y xfonts-100dpi xfonts-75dpi xfonts-scalable xfonts-cyrillic
RUN apt-get install -y python-matplotlib

RUN pip install numpy cython scipy h5py nibabel nipype
RUN pip install cvxpy scikit-learn
RUN pip install dipy joblib pandas nibabel

RUN pip install xvfbwrapper
RUN apt-get install -y python-vtk