royhaast/MP2RAGE-pipeline

MRI analysis pipeline optimized for submillimeter MP2RAGE datasets

MP2RAGE analysis pipeline

High-res analysis pipeline for MP2RAGE data, losely based on HCP's anatomical pipeline.

Software requirements:

- FSL (5.0)
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
	
- ANTs (latest release)
https://github.com/stnava/ANTs

- CBS tools (including MIPAV and JIST, latest releases)
https://www.nitrc.org/projects/cbs-tools/
https://mipav.cit.nih.gov/

- FreeSurfer v6.0 (stable)
https://surfer.nmr.mgh.harvard.edu/

- B1 correction code from J.P. Marques (and MATLAB)
https://github.com/JosePMarques/MP2RAGE-related-scripts

Tested on Linux system with:

- 32 gb RAM
- 16 cores
- GPU CUDA v5.0 installed
- Debian Wheezy (necessary for CUDA support)

Total processing time per subject: 8-9 hrs