IUSM-connectivity-pipeline

NOTE: This is legacy version of the IU School of Medicine Connectivity Pipeline dependent on Matlab. A refactored version of this pipeline written in Python and Bash is available here: https://github.com/IUSCA/IUSM-ConnPipe

Contributors:

• Evgeny Chumin, Indiana University School of Medicine, 2020
• Andrea Avena Koenigsberger, IU SCA, 2020
• John West, Indiana University School of Medicine, 2018
• Zikai Lin, Indiana University School of Medicine, 2018
• Mario Dzemidzic, Indiana University School of Medicine, 2018
• Joaquin Goni, Purdue University, 2018
• Enrico Amico, Purdue University, 2018

Description:

Executes pre-processing of anatomical, functional, and diffusion Magnetic Resonance Imaging data.

Requirements:

This code has been developed to operate with the following software:

• FSL version 5.0.10/11 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
• AFNI https://afni.nimh.nih.gov/
• dcm2niix (part of MRIcroGL) https://github.com/rordenlab/dcm2niix
• Camino http://camino.cs.ucl.ac.uk/
• Camino-TrackVis https://www.nitrc.org/projects/camino-trackvis/

Usage:

Located within the 'template_batch_files' subdirectory are two matlab script files:

• 'batch_setup.m'
• 'system_and_sample_setup_local.m'

These files must be modified to contain approporiate paths for your software and data. They also contain extensive documentation on usage, directory structure set-up, software requirements, etc... We recommend that these files are copied to a separate project directory, where they can be easily associated with your data.

Once modified, the 'run_connectivity_pipeline.m' function can be ran. Through the file selection user interface, select your modified files one at a time, after which processing will begin.

Pertinent References:

under construction