FreeSurfer Tutorial

Table of Contents

Section

Page

Overview and course outline

3

Inspection of Freesurfer output

5

Troubleshooting your output

22

Fixing a bad skull strip

26

Making edits to the white matter

34

Correcting pial surfaces

46

Using control points to fix intensity normalization

50

Talairach registration

55

recon-all: morphometry and reconstruction

69

recon-all: process flow table

97

QDEC Group analysis

100

Group analysis: average subject, design matrix, mri_glmfit

125

Group analysis: visualization and inspection

149

Integrating FreeSurfer and FSL's FEAT

159

Exercise overview

172

Tkmedit reference

176

Tksurfer reference

211

Glossary

227

References

229

Acknowledgments

238


2008-06-01 20:47