Beauchamp:Lab Notebook

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#[[Beauchamp:Subjects|Information for Subjects]]
#[[Beauchamp:Subjects|Information for Subjects]]
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==MRI==
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==MRI: Cortical Surface Models==
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#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
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#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
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#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
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#[[Beauchamp:SurfaceMetrics|Finding Closest node on the Surface]]
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#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
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#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
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#[[Beauchamp:CreateStndSurfModNew|Creating Standardized Surface Models]]
#[[Beauchamp:CreateStndSurfModNew|Creating Standardized Surface Models]]
#[[Beauchamp:FSStndSurf|FreeSurfer Standard Surface Models]]
#[[Beauchamp:FSStndSurf|FreeSurfer Standard Surface Models]]
 +
#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
 +
#[[Beauchamp:SurfaceMetrics|Finding Closest node on the Surface]]
 +
#[[Beauchamp:SUMA|SUMA]]
 +
#[[Beauchamp:FreeSurfer|Free Surfer]]
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#[[Beauchamp:Caret|Caret]]
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 +
==MRI: fMRI Analysis Stream==
 +
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
 +
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
 +
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
 +
#[[Beauchamp:AFNI|AFNI]]
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 +
==MRI: DTI Analysis==
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
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#[[Beauchamp:AFNI|AFNI]]
 
-
#[[Beauchamp:SUMA|SUMA]]
 
-
#[[Beauchamp:FreeSurfer|Free Surfer]]
 
-
#[[Beauchamp:Caret|Caret]]
 
-
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
 
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#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
 
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#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
 
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#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
 
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#[[Beauchamp:MVPA Notes|MVPA Notes]]
 
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#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
 
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#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
 
==TMS/TMS+MRI==
==TMS/TMS+MRI==
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#[[Beauchamp:Stimuli|McGurk Stimuli]]
#[[Beauchamp:Stimuli|McGurk Stimuli]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:Autism|Autism Data]]
 +
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
 +
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
 +
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
 +
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
 +
#[[Beauchamp:MVPA Notes|MVPA Notes]]
 +
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
 +
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]

Revision as of 16:12, 27 August 2010

Brain picture
Beauchamp Lab



Contents

General Notes

  1. How To Install Software and set up new computers
  2. How To order things for the lab

Subject Forms

  1. Information for Subjects

MRI: Cortical Surface Models

  1. Preparation for Creating Cortical Surface Models
  2. Creating Cortical Surface Models
  3. Using Cortical Surface Models
  4. What If a Cortical Surface Model Exists Already
  5. What If Cortical Surface Model Looks Bad
  6. Creating Standardized Surface Models
  7. FreeSurfer Standard Surface Models
  8. Finding Distances on the Surface
  9. Finding Closest node on the Surface
  10. SUMA
  11. Free Surfer
  12. Caret

MRI: fMRI Analysis Stream

  1. Overview of fMRI Analysis
  2. Motion and Distortion Correction
  3. Creating AFNI BRIKs from MR Data
  4. Creating Volume Average Datasets with AFNI
  5. AFNI

MRI: DTI Analysis

  1. Processing Diffusion Tensor Imaging Data
  2. Automatic VOI Initialization for Interactive Tractography
  3. Deterministic Tractography Constrained by Image Masks

TMS/TMS+MRI

  1. Notes on TMS


Electrophysiology/Electrophysiology+MRI

  1. Electrode Localization and Naming
  2. Electrophysiology Protocols
  3. Analyzing ECoG data (by Adam Burch)


Psychophysics

  1. New Auditory Tactile Experiment
  2. d' (d-prime) Analysis
  3. Race Model Analysis

Misc. Experiment Notes

  1. McGurk Stimuli
  2. Autism Data
  3. Scanner Stimulus and Eye Tracker Setup
  4. Retinotopic Mapping
  5. AFNI Atlas Values
  6. Tactile Experiment Notes
  7. MVPA Notes
  8. RealTimefMRI
  9. Notes on analyzing MRI data (old)
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