Diff for "FsTutorial/Exercises"

Differences between revisions 1 and 9 (spanning 8 versions)

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.

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

Exercise B. Resampling the parametric map onto a surface

Exercise C. Visualizing and navigating results

-  ⇤ ← Revision 1 as of 2005-08-10 13:12:35 → 
  Size: 2068
  Editor: NickSchmansky
  Comment:
+   ← Revision 9 as of 2008-04-29 11:45:41 → ⇥
  Size: 2683
  Editor: localhost
  Comment: converted to 1.6 markup
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-[wiki:Self:FsTutorial top]
+[[FsTutorial|top]]
 Line 5:
-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.
 Line 7:
-=== 1.0 Morphometry and reconstruction ===
+=== 1.0 Morphometry and Reconstruction ===
 Line 9:
-[wiki:Self:FsTutorial/Conversion Exercise A: Convert a DICOM volume into mgz format]
+[[FsTutorial/Conversion|Exercise A: Convert a DICOM volume into mgz format]]
 Line 11:
-[wiki:Self:FsTutorial/Talairach Exercise B: Fixing bad output from the Talairach registration]
+[[FsTutorial/Talairach|Exercise B: Fixing bad output from the Talairach registration]]
 Line 13:
-[wiki:Self:FsTutorial/ControlPoints Exercise C: Using control points for intensity normalization]
+[[FsTutorial/ControlPoints|Exercise C: Using control points for intensity normalization]]
 Line 15:
-[wiki:Self:FsTutorial/SkullStripTutorial Exercise D: Fixing bad output from skull stripping]
+[[FsTutorial/SkullStripFix|Exercise D: Fixing bad output from skull stripping]]
 Line 17:
-[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]]
 Line 19:
-[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]]
 Line 21:
-[wiki:Self:FsTutorial/PialEdits Exercise G: Correcting Pial Surfaces]
+[[FsTutorial/PialEdits|Exercise G: Correcting Pial Surfaces]]
 Line 23:
-[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]]
 Line 25:
-=== 2.0 Group analysis ===
 
[wiki:Self:FsTutorial/CreateFsgdFile Exercise A. Create an FSGD file using the table above]
+=== 2.0 Group Analysis ===
-Line 29:
+Line 27:
-[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]]
-Line 31:
+Line 29:
-[wiki:Self:FsTutorial/CreateContrastVectors Exercise C. Specify contrast vectors to test hypotheses]
+[[FsTutorial/CreateContrastVectors|Exercise B. Specify contrast vectors to test hypotheses]]
-Line 33:
+Line 31:
-[wiki:Self:FsTutorial/ComputeContrast Exercise D. Use mris_glm to compute the contrast]
+[[FsTutorial/ComputeContrast|Exercise C. Use mris_glm to compute the contrast]]
-Line 35:
+Line 33:
-=== 3.0 Visualization and inspection of group analysis results ===
+=== 3.0 Visualization and Inspection of Group Analysis Results ===
-Line 37:
+Line 35:
-[wiki:Self:FsTutorial/VisualizingAndPlotting Exercise A. Visualizing and plotting]
+[[FsTutorial/Visualization|Exercise A. Visualizing and plotting]]
-Line 39:
+Line 37:
-[wiki:Self:FsTutorial/ComputingRoiStatistics Exercise B. Computing statistics inside an ROI]
+=== 4.0 Working with FSL Feat Output and FreeSurfer ===
-Line 41:
+Line 39:
-=== 4.0 Working with FSL Feat output and FreeSurfer ===
+[[FsTutorial/RegisterFeatOntoAnatomical|Exercise A. Registering FSL Feat output to the anatomical]]
-Line 43:
+Line 41:
-[wiki:Self:FsTutorial/RegisterFeatOntoAnatomical Exercise A. Registering FSL Feat output to the anatomical]
+[[FsTutorial/OverlayFeatStatisticalMaps|Exercise B. Overlaying FSL Feat statistical maps]]
-Line 45:
+Line 43:
-[wiki:Self:FsTutorial/OverlayFeatStatisticalMaps Exercise B. Overlaying FSL Feat statistical maps]
+[[FsTutorial/MapSegmentationsToFunctionalSpace|Exercise C. Mapping automatic segmentations to the functional space]]
-Line 47:
+Line 45:
-[wiki:Self:FsTutorial/MapSegmentationsToFunctionalSpace Exercise C. Mapping automatic segmentations to the functional space]
+=== 5.0 Working with SPM Output and FreeSurfer ===
-Line 49:
+Line 47:
+==== 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]]