Beauchamp:Lab Notebook: Difference between revisions

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#[http://129.106.236.9:8888/mediawiki/index.php/Main_Page Internal Wiki (UTHSC-H Only)]
To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type
  site:openwetware.org/wiki/Beauchamp ExperimentSheet


==MRI==
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Ordering|How To order things for the lab]]
 
==Experimental Design and Analysis==
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[Beauchamp:HowToScan|How to Collect MRI Data and Use the Scanner]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
#[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]]
#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
#[[Beauchamp:MVPA Notes|MVPA Notes]]
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
#[[Beauchamp:GroupAna|Group Analysis with Unequal Group Sizes using GroupAna.m]]
#[[Beauchamp:UseCortSurfMod|Using Cortical Surface Models]]
#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
#[[Beauchamp:ROIanalysis|ROI Analysis]]


==Electrophysiology Protocols==
==MRI: DTI Analysis==
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]


[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
==TMS/TMS+MRI==
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]


==Behavioral Experiments==  
==NIRS==
[[Beauchamp:AuditoryTactile|New Auditory Tactile Experiment]]
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]


==Electrophysiology/Electrophysiology+MRI==
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Beauchamp:ECogAnalysisv2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[Making Resting State Correlation Maps]]


==Ordering==  
==Psychophysics==  
G Power 3 is a useful program for power analysis
http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/
#[[Beauchamp:AuditoryTactile|New Auditory Tactile Experiment]]
#[[Beauchamp:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:RaceModel|Race Model Analysis]]
#[[Beauchamp:100Hue|Stimuli for 100 Hue Experiment]]
#[[Beauchamp:CIMS|Causal Inference model for Synchrony Perception]]
#[[Beauchamp:NED|Predicting McGurk Fusion Rates]]


[[Beauchamp:Ordering|Ordering]]
==Misc. Experiment Notes==
#[[Beauchamp:Stimuli|McGurk Stimuli]]
#[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]

Revision as of 12:19, 9 September 2014

Brain picture
Beauchamp Lab




To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type 

 site:openwetware.org/wiki/Beauchamp ExperimentSheet

General Important Notes

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

Experimental Design and Analysis

  1. Overview of MRI Experiments
  2. Information for Subjects and Experimenters, such as Human Subjects Training
  3. How to Collect MRI Data and Use the Scanner
  4. Getting raw data from the scanner
  5. Turning the raw data into AFNI BRIKs
  6. Cortical Surface models overview
  7. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  8. Motion and Distortion Correction
  9. Creating Volume Average Datasets with AFNI
  10. MVPA Notes
  11. RealTimefMRI
  12. Group Analysis with Unequal Group Sizes using GroupAna.m
  13. HiResolution fMRI
  14. ROI Analysis

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. Overview of an MRI/fMRI guided TMS Experiment
  2. Notes on TMS

NIRS

  1. Eswen Fava's NIRS Manual

Electrophysiology/Electrophysiology+MRI

  1. Beauchamp:Electrode Localization and Naming
  2. Electrophysiology Protocols
  3. Analyzing ECoG data (by Adam Burch)
  4. Analyzing ECoG data (by Muge Ozker Sertel)
  5. Making Resting State Correlation Maps

Psychophysics

G Power 3 is a useful program for power analysis http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/

  1. New Auditory Tactile Experiment
  2. d' (d-prime) Analysis
  3. Race Model Analysis
  4. Stimuli for 100 Hue Experiment
  5. Causal Inference model for Synchrony Perception
  6. Predicting McGurk Fusion Rates

Misc. Experiment Notes

  1. McGurk Stimuli
  2. Word Localizer Stimuli
  3. Autism Data
  4. SR EyeLink Eye Tracker Setup
  5. OLD ASL Eye Tracker Setup
  6. Retinotopic Mapping
  7. AFNI Atlas Values
  8. Tactile Experiment Notes
  9. Notes on analyzing MRI data (old)
  10. ANOVAs in MATLAB
  11. HNL Projector Settings
  12. Notes on Stimulus Projector and Screen in UT Philips Scanner
  13. Auditory-only stimuli
  14. Video Stimulus Creation
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