- Evgeny Chumin, Indiana University School of Medicine, 2018
- 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
Executes pre-processing of anatomical, functional, and diffusion Magnetic Resonance Imaging data.
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/
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.
under construction