Difference between revisions of "Beauchamp:Lab Notebook"

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(Experimental Design and Analysis)
 
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==General Important Notes==
 
==General Important Notes==
 +
#[[Beauchamp:Orientation|Guide for new lab members]]
 
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
 
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
 +
#[[Beauchamp:AFNI_Install|How To Install AFNI]]
 
#[[Beauchamp:Ordering|How To order things for the lab]]
 
#[[Beauchamp:Ordering|How To order things for the lab]]
 +
#[[Beauchamp:CAMRI_PTS|Sign-up for CAMRI Project Tracking System]]
  
 
==Experimental Design and Analysis==
 
==Experimental Design and Analysis==
 +
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
 
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
 
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
 
 
#[[Beauchamp:HowToScan|How to Collect MRI Data and Use the Scanner]]
 
#[[Beauchamp:HowToScan|How to Collect MRI Data and Use the Scanner]]
 
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
 
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
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#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
 
#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
 
#[[Beauchamp:ROIanalysis|ROI Analysis]]
 
#[[Beauchamp:ROIanalysis|ROI Analysis]]
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#[[Beauchamp:AutomatingAFNI|Automating AFNI and SUMA]]
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#[[Finding Release Burst Duration]]
  
 
==MRI: DTI Analysis==
 
==MRI: DTI Analysis==
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#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
 
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
 
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
 
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
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#[[Beauchamp: Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
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#[[Beauchamp:ALICE|Electrode Localization using steps from the ALICE package]]
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#[[Beauchamp:img_pipe|Electrode Localization using steps from the img_pipe package]]
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#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
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#[[Beauchamp:ActivityMaps|Making Activity Maps]]
 
#[[Making Resting State Correlation Maps]]
 
#[[Making Resting State Correlation Maps]]
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#[[Beauchamp:TensorECOG|Tensor Analysis of ECOG data]]
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#[[Beauchamp:Tobii|Using Tobii Eye Tracking Glasses]]
  
 
==Psychophysics==  
 
==Psychophysics==  
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#[[Beauchamp:100Hue|Stimuli for 100 Hue Experiment]]
 
#[[Beauchamp:100Hue|Stimuli for 100 Hue Experiment]]
 
#[[Beauchamp:CIMS|Causal Inference model for Synchrony Perception]]
 
#[[Beauchamp:CIMS|Causal Inference model for Synchrony Perception]]
#[[Beauchamp:MCG_Predict|Predicting McGurk Fusion Rates]]
+
#[[Beauchamp:NED|Predicting McGurk Fusion Rates]]
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#[[Beauchamp:Playback Rate|Effect of Video Playback Rate on McGurk Fusion Rates]]
  
 
==Misc. Experiment Notes==  
 
==Misc. Experiment Notes==  
 +
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation  ]
 
#[[Beauchamp:Stimuli|McGurk Stimuli]]
 
#[[Beauchamp:Stimuli|McGurk Stimuli]]
 +
#[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]]
 
#[[Beauchamp:Autism|Autism Data]]
 
#[[Beauchamp:Autism|Autism Data]]
 
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
 
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
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#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
 
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
 
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]
 
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]
 +
#[[Beauchamp:PrintingBrains|How to 3D Print Brains]]
 +
#[[Beauchamp:TensorECOG|RHOPLS for ECoG Data]]

Latest revision as of 10:12, 3 November 2017

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. Guide for new lab members
  2. How To Install Software and set up new computers
  3. How To Install AFNI
  4. How To order things for the lab
  5. Sign-up for CAMRI Project Tracking System

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
  15. Automating AFNI and SUMA
  16. Finding Release Burst Duration

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. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  5. Electrode Localization using steps from the ALICE package
  6. Electrode Localization using steps from the img_pipe package
  7. Analyzing ECoG data (by Muge Ozker Sertel)
  8. Making Activity Maps
  9. Making Resting State Correlation Maps
  10. Tensor Analysis of ECOG data
  11. Using Tobii Eye Tracking Glasses

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
  7. Effect of Video Playback Rate on McGurk Fusion Rates

Misc. Experiment Notes

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