Beauchamp:Lab Notebook

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(MRI: fMRI Experimental Design and Analysis)
Current revision (09:34, 30 October 2014) (view source)
(Electrophysiology/Electrophysiology+MRI)
 
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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==
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
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#[[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]]
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#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
 
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==MRI: fMRI Experimental Design and Analysis==
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==Experimental Design and Analysis==
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#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
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#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
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#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[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]]
#[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]]
#[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]]
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#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
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#[[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:MVPA Notes|MVPA Notes]]
#[[Beauchamp:MVPA Notes|MVPA Notes]]
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==Electrophysiology/Electrophysiology+MRI==
==Electrophysiology/Electrophysiology+MRI==
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#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrode Localization and Naming]]
#[[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: 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: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]]
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#[[Beauchamp:MCG_Predict|Predicting McGurk Fusion Rates]]
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#[[Beauchamp:NED|Predicting McGurk Fusion Rates]]
==Misc. Experiment Notes==  
==Misc. Experiment Notes==  
#[[Beauchamp:Stimuli|McGurk Stimuli]]
#[[Beauchamp:Stimuli|McGurk Stimuli]]
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#[[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]]
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==MRI: Cortical Surface Models==
 
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There is a simple three step process for creating surface models. The steps assume that you are in the afni subdirectory of the subject for which a surface is to be created.
 
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  cd /Volumes/data/UT/IZ/afni
 
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Step 1: Prepare the FreeSurfer directory tree
 
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  /Volumes/data/scripts/@prep_dir IZanatavg+orig.BRIK 
 
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Step 2: Reconstruct the surface. Note that the name of the anatomy is not needed, but if you are using the up arrow in the UNIX shell to recall the last command and edit it, there is no need to delete the filename. This step takes many hours!
 
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  /Volumes/data/scripts/@recon IZanatavg+orig.BRIK
 
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Step 3: Finish the surface
 
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  /Volumes/data/scripts/@finish IZanatavg+orig.BRIK
 
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step 4: Check the created surface
 
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  cd ..
 
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  ./@ec
 
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Or in a more economical way:
 
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  set ec = IZ
 
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  cd /Volumes/data/UT/{$ec}/afni
 
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  /Volumes/data/scripts/@prep_dir {$ec}anatavg+orig.BRIK 
 
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  /Volumes/data/scripts/@recon {$ec}anatavg+orig.BRIK
 
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  /Volumes/data/scripts/@finish {$ec}anatavg+orig.BRIK
 
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  cd ..
 
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  ./@ec
 
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For more details, see the following web pages:
 
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#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
 
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#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
 
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#[[Beauchamp:UseCortSurfMod|Final touches and using Cortical Surface Models]]
 
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#[[Beauchamp:IfCortModExists|What If a Cortical Surface Model Exists Already]]
 
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#[[Beauchamp:EditingCortSurf|What If Cortical Surface Model Looks Bad]]
 
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#[[Beauchamp:CreateStndSurfModNew|Creating Standardized Surface Models]]
 
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#[[Beauchamp:FSStndSurf|FreeSurfer Standard Surface Models]]
 
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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:SUMA|SUMA]]
 
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#[[Beauchamp:FreeSurfer|Free Surfer]]
 
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#[[Beauchamp:Caret|Caret]]
 

Current revision

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

Contents

General Important Notes

  1. How To Install Software and set up new computers
  2. How To Install AFNI
  3. 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. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  5. Analyzing ECoG data (by Muge Ozker Sertel)
  6. Making Activity Maps
  7. 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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