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| [wiki:Self:FsTutorial top] | [[FsTutorial|top]] |
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| Below are links to the tutorial exercises, extracted from the tutorial's supporting text. | 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. |
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| [wiki:Self:FsTutorial/Conversion Exercise A: Convert a DICOM volume into mgz format] | [[FsTutorial/Conversion|Exercise A: Convert a DICOM volume into mgz format]] |
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| [wiki:Self:FsTutorial/Talairach Exercise B: Fixing bad output from the Talairach registration] | [[FsTutorial/Talairach|Exercise B: Fixing bad output from the Talairach registration]] |
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| [wiki:Self:FsTutorial/ControlPoints Exercise C: Using control points for intensity normalization] | [[FsTutorial/ControlPoints|Exercise C: Using control points for intensity normalization]] |
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| [wiki:Self:FsTutorial/SkullStripTutorial Exercise D: Fixing bad output from skull stripping] | [[FsTutorial/SkullStripFix|Exercise D: Fixing bad output from skull stripping]] |
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| [wiki:Self:FsTutorial/ViewSegOutput Exercise E: View each of the volumes produced after the preprocessing steps with tkmedit] | [[FsTutorial/ViewSegOutput|Exercise E: View each of the volumes produced after the preprocessing steps with tkmedit]] |
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| [wiki:Self:FsTutorial/FixingDefects Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces] | [[FsTutorial/WhiteMatterEdits|Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces]] |
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| [wiki:Self:FsTutorial/PialEdits Exercise G: Correcting Pial Surfaces] | [[FsTutorial/PialEdits|Exercise G: Correcting Pial Surfaces]] |
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| [wiki:Self:FsTutorial/FinalSurfEx Exercise H: View the final surfaces with tkmedit and tksurfer] | [[FsTutorial/FinalSurfEx|Exercise H: View the final surfaces with tkmedit and tksurfer]] |
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| [wiki:Self:FsTutorial/CreateFsgdFile Exercise A. Create an FSGD file using the table above] | |
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| [wiki:Self:FsTutorial/PerformEstimation Exercise B. Use mris_glm to perform the estimation] | [[FsTutorial/CreateFsgdFile|Exercise A. Create an FSGD file using the table above]] |
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| [wiki:Self:FsTutorial/CreateContrastVectors Exercise C. Specify contrast vectors to test hypotheses] | [[FsTutorial/CreateContrastVectors|Exercise B. Specify contrast vectors to test hypotheses]] |
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| [wiki:Self:FsTutorial/ComputeContrast Exercise D. Use mris_glm to compute the contrast] | [[FsTutorial/ComputeContrast|Exercise C. Use mris_glm to compute the contrast]] |
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| [wiki:Self:FsTutorial/VisualizingAndPlotting Exercise A. Visualizing and plotting] | [[FsTutorial/Visualization|Exercise A. Visualizing and plotting]] |
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| [wiki:Self:FsTutorial/ComputingRoiStatistics Exercise B. Computing statistics inside an ROI] | === 4.0 Working with FSL Feat Output and FreeSurfer === |
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| === 4.0 Functional Registration === | [[FsTutorial/RegisterFeatOntoAnatomical|Exercise A. Registering FSL Feat output to the anatomical]] |
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| [wiki:Self:FsTutorial/ManualRegistration Exercise A. Experimenting with manual registration] | [[FsTutorial/OverlayFeatStatisticalMaps|Exercise B. Overlaying FSL Feat statistical maps]] |
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| [wiki:Self:FsTutorial/AutomaticRegistrationSpm Exercise B. Automatic registration using spmregister and verifying results with qmedit] | [[FsTutorial/MapSegmentationsToFunctionalSpace|Exercise C. Mapping automatic segmentations to the functional space]] |
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| === 5.0 Functional Overlay === | === 5.0 Working with SPM Output and FreeSurfer === |
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| [wiki:Self:FsTutorial/OverlayFuncMapOntoStructural Exercise A. Visualizing the parametric map overlayed onto structural data] | ==== 5.1 Functional Registration ==== |
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| [wiki:Self:FsTutorial/ResampleFuncParametricMap Exercise B. Resampling the parametric map onto a surface] | [[FsTutorial/ManualRegistration|Exercise A. Experimenting with manual registration]] |
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| [wiki:Self:FsTutorial/NavigateResampledParametricMap Exercise C. Visualizing and navigating results] | [[FsTutorial/AutomaticRegistrationSpm|Exercise B. Automatic registration using spmregister and verifying results with qmedit]] |
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| === 6.0 Working with FSL Feat Output and FreeSurfer === | ==== 5.2 Functional Overlay ==== |
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| [wiki:Self:FsTutorial/RegisterFeatOntoAnatomical Exercise A. Registering FSL Feat output to the anatomical] | [[FsTutorial/OverlayFuncMapOntoStructural|Exercise A. Visualizing the parametric map overlayed onto structural data]] |
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| [wiki:Self:FsTutorial/OverlayFeatStatisticalMaps Exercise B. Overlaying FSL Feat statistical maps] | [[FsTutorial/ResampleFuncParametricMap|Exercise B. Resampling the parametric map onto a surface]] |
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| [wiki:Self:FsTutorial/MapSegmentationsToFunctionalSpace Exercise C. Mapping automatic segmentations to the functional space] |
[[FsTutorial/NavigateResampledParametricMap|Exercise C. Visualizing and navigating results]] |
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 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
Exercise A: Convert a DICOM volume into mgz format
Exercise B: Fixing bad output from the Talairach registration
Exercise C: Using control points for intensity normalization
Exercise D: Fixing bad output from skull stripping
Exercise E: View each of the volumes produced after the preprocessing steps with tkmedit
Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces
Exercise G: Correcting Pial Surfaces
Exercise H: View the final surfaces with tkmedit and tksurfer
2.0 Group Analysis
Exercise A. Create an FSGD file using the table above
Exercise B. Specify contrast vectors to test hypotheses
Exercise C. Use mris_glm to compute the contrast
3.0 Visualization and Inspection of Group Analysis Results
Exercise A. Visualizing and plotting
4.0 Working with FSL Feat Output and FreeSurfer
Exercise A. Registering FSL Feat output to the anatomical
Exercise B. Overlaying FSL Feat statistical maps
Exercise C. Mapping automatic segmentations to the functional space
5.0 Working with SPM Output and FreeSurfer
5.1 Functional Registration
Exercise A. Experimenting with manual registration
Exercise B. Automatic registration using spmregister and verifying results with qmedit
5.2 Functional Overlay
Exercise A. Visualizing the parametric map overlayed onto structural data