[[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 [[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 ===

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

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

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

[[FsTutorial/SkullStripFix|Exercise D: Fixing bad output from skull stripping]]

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

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

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

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

=== 2.0 Group Analysis ===

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

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

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

=== 3.0 Visualization and Inspection of Group Analysis Results ===

[[FsTutorial/Visualization|Exercise A. Visualizing and plotting]]

=== 4.0 Working with FSL Feat Output and FreeSurfer ===

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

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

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

=== 5.0 Working with SPM Output and FreeSurfer ===

==== 5.1 Functional Registration ====

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

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

==== 5.2 Functional Overlay ====

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

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

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