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| [wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial top] |
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| === 1.0 Morphometry and reconstruction === | === 1.0 Morphometry and Reconstruction === |
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| [wiki:Self:FsTutorial/FixingDefects Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces] | [wiki:Self:FsTutorial/FixingGeomInaccuracies Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces] |
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| === 2.0 Group analysis === |
=== 2.0 Group Analysis === |
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| [wiki:Self:FsTutorial/PerformEstimation Exercise B. Use mris_glm to perform the estimation] | [wiki:Self:FsTutorial/CreateContrastVectors Exercise B. Specify contrast vectors to test hypotheses] |
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| [wiki:Self:FsTutorial/CreateContrastVectors Exercise C. Specify contrast vectors to test hypotheses] | [wiki:Self:FsTutorial/ComputeContrast Exercise C. Use mris_glm to compute the contrast] |
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| [wiki:Self:FsTutorial/ComputeContrast Exercise D. Use mris_glm to compute the contrast] === 3.0 Visualization and inspection of group analysis results === |
=== 3.0 Visualization and Inspection of Group Analysis Results === |
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| === 4.0 Working with FSL Feat output and FreeSurfer === | === 4.0 Working with FSL Feat Output and FreeSurfer === |
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| === 5.0 Working with SPM Output and FreeSurfer === ==== 5.1 Functional Registration ==== [wiki:Self:FsTutorial/ManualRegistration Exercise A. Experimenting with manual registration] [wiki:Self:FsTutorial/AutomaticRegistrationSpm Exercise B. Automatic registration using spmregister and verifying results with qmedit] ==== 5.2 Functional Overlay ==== [wiki:Self:FsTutorial/OverlayFuncMapOntoStructural Exercise A. Visualizing the parametric map overlayed onto structural data] [wiki:Self:FsTutorial/ResampleFuncParametricMap Exercise B. Resampling the parametric map onto a surface] [wiki:Self:FsTutorial/NavigateResampledParametricMap Exercise C. Visualizing and navigating results] |
[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/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]