Exercise Overview

Below are links to the tutorial exercises, extracted from the tutorial's supporting text. To follow these exercises exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own paths and subject names.

1.0 Morphometry and Reconstruction

Exercise A: Convert a DICOM volume into mgz format

Exercise B: Fixing bad output from the Talairach registration

Exercise C: Using control points for intensity normalization

Exercise D: Fixing bad output from skull stripping

Exercise E: View each of the volumes produced after the preprocessing steps with tkmedit

Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces

Exercise G: Correcting Pial Surfaces

Exercise H: View the final surfaces with tkmedit and tksurfer

2.0 Group Analysis

Exercise A. Create an FSGD file using the table above

Exercise B. Specify contrast vectors to test hypotheses

Exercise C. Use mris_glm to compute the contrast

3.0 Visualization and Inspection of Group Analysis Results

Exercise A. Visualizing and plotting

4.0 Working with FSL Feat Output and FreeSurfer

Exercise A. Registering FSL Feat output to the anatomical

Exercise B. Overlaying FSL Feat statistical maps

Exercise C. Mapping automatic segmentations to the functional space

5.0 Working with SPM Output and FreeSurfer

5.1 Functional Registration

Exercise A. Experimenting with manual registration

Exercise B. Automatic registration using spmregister and verifying results with qmedit

5.2 Functional Overlay

Exercise A. Visualizing the parametric map overlayed onto structural data

Exercise B. Resampling the parametric map onto a surface

Exercise C. Visualizing and navigating results

FsTutorial/Exercises (last edited 2008-04-29 11:45:41 by localhost)