[wiki:FsTutorial top]

Exercise Overview

Below are links to the tutorial exercises, extracted from the tutorial's supporting text.

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/FixingDefects 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/PerformEstimation Exercise B. Use mris_glm to perform the estimation]

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

[wiki:FsTutorial/ComputeContrast Exercise D. 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]