FSL & FreeSurfer Course

2009 Lectures and Practicals

• The following links to individual talks and practical instructions are printable PDF or HTML files.
• Alternatively, lectures.tar.gz contains all of this (the FSL & FreeSurfer lectures and practical instructions) in a single download.

Data Files:

• Data for the FSL practicals (in 5 parts due to large size): 1-2-3-4-5. (Internal FMRIB people - see here for information on how to follow this course on your own inside FMRIB.)
• The files contain data for the following practicals: 1 = intro, registration, structural/segmentation and scripting; 2 = melodic, diffusion (fdt + tbss); 3 = fmri (excluding one 3 level example); 4 = fmri (3 level controls); 5 = fmri (3 level patients).

• Introduction to Imaging, FSL & FreeSurfer   lecture part 1, part 2 / practical

• Brain Extraction, Registration, Motion Correction and EPI Distortion   (BET, FLIRT, MCFLIRT, PRELUDE&FUGUE)   lecture / practical

• FMRI Preprocessing and Model-Based Analysis  (FEAT)
  • 1. Preprocesing and Simple Single-Session Stats   lecture part 1, part 2 / practical
  • 2. Advanced Single-Session Stats   lecture / practical
  • 3. Multi-Session FMRI   lecture / practical

• Randomise lecture

• Segmentation & Structural Statistics  (FAST, FIRST, SIENA, FSL-VBM) lecture / practical

• Model-Free FMRI Analysis  (MELODIC)  lecture / practical

• Analysis of Diffusion-Weighted MR Data  (FDT, TBSS)  lecture / practical

• Scripting  lecture & practical. This is not a formal part of the course, but can be carried out on your own during the course if you have time to spare. Within the lecture web pages, to find the interleaved practical instructions, click on the e symbols when they appear in the lecture slides, or go to the lecture index (via the up arrow in the bottom right) and find the green links.

• Introduction to FreeSurfer
• FreeSurfer Applications
• Cortical Reconstruction
• Surface-based Group Analysis
• FreeSurfer: Failure Modes and Interventions
• FSL-FreeSurfer Integration
• Freesurfer: Future Directions
• FreeSurfer Tutorial

Additional Lectures

• Karla Miller: MRI Physics & Diffusion Physics

• Andreas Bartsch: Advanced Clinial (F)MRI Applications of FSL
• Susan Bookheimer: FMRI Experimental Design
• Susan Bookheimer: Clinical Applications of FMRI
• Mark Cohen: Magnetic Resonance Imaging basics and fmri
• Nicola De Stefano: Clinical Applications of Structural MRI
• Kate Watkins: Experimental Design
• Richard Wise: FMRI Acquisition

Additional Reading Material

People with no previous experience of UNIX would benefit greatly from spending a few hours, before coming, working through at least the first 5 sections of A Basic UNIX Tutorial.

People with no background in FMRI experimentation and analysis would probably benefit from reading Chapters 1,9-16 from Functional MRI: An Introduction to Methods (or order at Amazon UK / USA).