This course aims to provide an overview of the FreeSurfer recon-all pipeline for T1w MRI processing. By the end of the 5-day course, users will hopefully be able to tackle common errors that typically arise from running adolescent samples and confidently use FreeSurfer tools and outputs for their own analyses.
Main FreeSurfer website: http://www.freesurfer.net/
Recon-all Table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
Recon-all Wiki Page: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
This repository has several parts:
- Class Syllabus: In the main folder you'll find this document with a summary of what to expect from the class as well as out schedule for Winter 2017.
- Class Slides: After each Monday class I'll upload the slides from that week. Be sure to review them for reinforcement!
- Class Bin: Quick scripts and functions that I have written to make it easier to manually adjust the freesurfer recon-all pipeline.
- Extracting Data: MATLAB functions I've written to extract data from an entire project and export it into CSVs for analysis in SPSS, MATLAB, or any other statistics program.
- Practice Brains: These are brain images kindly donated by members of the lab to enable your learning. Please feel free to use these files to practice using FreeSurfer.