fMRI Data Analysis Using AFNI
Material from 2005 Spring Seminar given by Aaron Newman
IDEA Programming Documentation
Rational Rose Model documentation for IDEA
BCS 512 - Spins to Brains
Download data sets for assignment
(These files are also available on machines in the RCBI workstation room in the /RCBI/FMRI_course_data directory.)
Block Subject Design
- block_subj01.zip [75 MB]
DTI Project
- DTI_project.zip [5 MB]
Event Related
- for_513.zip [246 MB]
Retinotopic Mapping
- Instructions for installing and using retinotopic mapping software can be found on the retinotopy webpage
- class-P4-data.zip[209 MB]
Volumetric Analysis
- Class slides about Segmentation If you would like to see the animations of the brain that were originally shown with the slides, you will need to download them here and here. If you do not download the animation, PowerPoint may give you an error message about the missing movie files "Movie-GM-2.mpg" and "SagSeg.mpg"
- Volumetric-Dataset.zip[31 MB]
FSL and FreeSurfer
FSL and FreeSurfer Course Slides
FEAT Manual
FSL Course Data
- If you are using the RCBI machines, the course data can be found in /RCBI/fsl_course_data
- If you are using your own machine, you can download the 436 MB dataset.
FSL Documentation
- Introduction
- FDT - FMRIB's Diffusion Toolbox
- FLIRT, MCFLIRT and FUGUE - Registration, Motion Correction and EPI Distortion
- FMRI Preprocessing and Model-Based Analysis
- MELODIC (Multivariate Exploratory Linear Optimised Decomposition into Independent Components) - Model-free Functional Data Analysis
- Shell Scripting
- Structural Analysis: Segmentation and Statistics
Lectures by Matthijs Vink
Pre-processing and Analysis of Functional MRI Data: