Beauchamp:Lab Notebook: Difference between revisions

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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]]
#[[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==
#[[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]]
==MRI: fMRI Experimental Design and Analysis==
#[[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: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]]
#[[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==
#[[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)]]
#[[Beauchamp: Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[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]]
#[[Beauchamp:MCG_Predict|Predicting McGurk Fusion Rates]]
#[[Beauchamp:NED|Predicting McGurk Fusion Rates]]
#[[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]]
==MRI: Cortical Surface Models==
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.
  cd /Volumes/data/UT/IZ/afni
Step 1: Prepare the FreeSurfer directory tree
  /Volumes/data/scripts/@prep_dir IZanatavg+orig.BRIK 
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!
  /Volumes/data/scripts/@recon IZanatavg+orig.BRIK
Step 3: Finish the surface
  /Volumes/data/scripts/@finish IZanatavg+orig.BRIK
step 4: Check the created surface
  cd ..
  ./@ec
Or in a more economical way:
  set ec = IZ
  cd /Volumes/data/UT/{$ec}/afni
  /Volumes/data/scripts/@prep_dir {$ec}anatavg+orig.BRIK 
  /Volumes/data/scripts/@recon {$ec}anatavg+orig.BRIK
  /Volumes/data/scripts/@finish {$ec}anatavg+orig.BRIK
  cd ..
  ./@ec
 
For more details, see the following web pages:
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
#[[Beauchamp:UseCortSurfMod|Final touches and using Cortical Surface Models]]
#[[Beauchamp:IfCortModExists|What If a Cortical Surface Model Exists Already]]
#[[Beauchamp:EditingCortSurf|What If Cortical Surface Model Looks Bad]]
#[[Beauchamp:CreateStndSurfModNew|Creating Standardized 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]]
#[[Beauchamp:Caret|Caret]]

Revision as of 20:51, 23 September 2016

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 Install AFNI
  3. How To order things for the lab
  4. 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

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
  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
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