app-roi2roitracking

This app will perform ensemble tracking between 2 or more cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. First, the ROIs are registered to diffusion space using Freesurfer's mri_label2vol, and a white matter mask is generated in diffusion space, by running the create_wm_mask script. Then, tracking will be performed using mrtrix/0.2.12 by running the trackROI2ROI script. Finally, a classification structure will be generated using Vistasoft's bsc_mergeFGandClass and bsc_makeFGsFromClassification functions by running the classificationGenerator script.

Authors

• Dan Bullock (dnbulloc@iu.edu)
• Brad Caron (bacaron@iu.edu)

Contributors

• Soichi Hayashi (hayashi@iu.edu)
• Franco Pestilli (franpest@indiana.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.191 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.

{
	"roiPairs":	"23 95 2 8\n1 2 12 34\n8 3 5\n4 5",
	"track":  "path/to/tck.tck",
	"atlas":  "path/to/atlas.nii.gz",
   	"smoothKernel": 0
}

Sample Datasets

You can download sample datasets from Brainlife using Brainlife CLI.

npm install -g brainlife
bl login
mkdir input

roi & atlas sample needed

3. Launch the App by executing main

./main

Output

The main outputs of this App is a 'track.tck' file, a folder called 'tracts' containing .json files for each tract, an 'classification.mat' containing the classification structure, and a text file called 'output_fibercounts.txt' which contains information regarding the number of streamlines in each tract.

Product.json

The secondary output of this app is product.json. This file allows web interfaces, DB and API calls on the results of the processing.

Dependencies

This App requires the following libraries when run locally.

• singularity: https://singularity.lbl.gov/
• VISTASOFT: https://github.com/vistalab/vistasoft/
• ENCODE: https://github.com/brain-life/encode
• SPM 8 or 12: https://www.fil.ion.ucl.ac.uk/spm/software/spm8/
• WMA: https://github.com/brain-life/wma
• Freesurfer: https://hub.docker.com/r/brainlife/freesurfer/tags/6.0.0
• mrtrix: https://hub.docker.com/r/brainlife/mrtrix_on_mcr/tags/1.0
• jsonlab: https://github.com/fangq/jsonlab.git