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[wiki:FsTutorial top]

## 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 [wiki:FsTutorial/Data 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

[wiki:FsTutorial/Conversion Exercise A: Convert a DICOM volume into mgz format]

[wiki:FsTutorial/Talairach Exercise B: Fixing bad output from the Talairach registration]

[wiki:FsTutorial/ControlPoints Exercise C: Using control points for intensity normalization]

[wiki:FsTutorial/SkullStripTutorial Exercise D: Fixing bad output from skull stripping]

[wiki:FsTutorial/ViewSegOutput Exercise E: View each of the volumes produced after the preprocessing steps with tkmedit]

[wiki:FsTutorial/FixingGeomInaccuracies Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces]

[wiki:FsTutorial/PialEdits Exercise G: Correcting Pial Surfaces]

[wiki:FsTutorial/FinalSurfEx Exercise H: View the final surfaces with tkmedit and tksurfer]

### 2.0 Group Analysis

[wiki:FsTutorial/CreateFsgdFile Exercise A. Create an FSGD file using the table above]

[wiki:FsTutorial/CreateContrastVectors Exercise B. Specify contrast vectors to test hypotheses]

[wiki:FsTutorial/ComputeContrast Exercise C. Use mris_glm to compute the contrast]

### 3.0 Visualization and Inspection of Group Analysis Results

[wiki:FsTutorial/VisualizingAndPlotting Exercise A. Visualizing and plotting]

[wiki:FsTutorial/ComputingRoiStatistics Exercise B. Computing statistics inside an ROI]

### 4.0 Working with FSL Feat Output and FreeSurfer

[wiki:FsTutorial/RegisterFeatOntoAnatomical Exercise A. Registering FSL Feat output to the anatomical]

[wiki:FsTutorial/OverlayFeatStatisticalMaps Exercise B. Overlaying FSL Feat statistical maps]

[wiki:FsTutorial/MapSegmentationsToFunctionalSpace Exercise C. Mapping automatic segmentations to the functional space]

### 5.0 Working with SPM Output and FreeSurfer

#### 5.1 Functional Registration

[wiki:FsTutorial/ManualRegistration Exercise A. Experimenting with manual registration]

[wiki:FsTutorial/AutomaticRegistrationSpm Exercise B. Automatic registration using spmregister and verifying results with qmedit]

#### 5.2 Functional Overlay

[wiki:FsTutorial/OverlayFuncMapOntoStructural Exercise A. Visualizing the parametric map overlayed onto structural data]

[wiki:FsTutorial/ResampleFuncParametricMap Exercise B. Resampling the parametric map onto a surface]

[wiki:FsTutorial/NavigateResampledParametricMap Exercise C. Visualizing and navigating results]

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