Beauchamp:Lab Notebook: Difference between revisions

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==MRI==
To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type
#[http://129.106.236.18:8888/mediawiki/index.php/Main_Page UT-Only Wiki]
  site:openwetware.org/wiki/Beauchamp ExperimentSheet
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]


==Electrophysiology Protocols==
==General Important Notes==
#[[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:CAMRI_PTS|Sign-up for CAMRI Project Tracking System]]


[[Beauchamp:Presurgical Scanning|Presurgical Scanning]]
==Experimental Design and Analysis==
 
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles.
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles; then the folders can be dragged from the server to Xfiles, or copied in the command line, easily (without using the Web-based GUI interface).
#[[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]]
<i>In the EMU</i>
#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]]
 
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
[[Beauchamp:Setup Apparatus|Setup Apparatus]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
 
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
[[Beauchamp:Receptive Field Mapping|Receptive Field Mapping]]
#[[Beauchamp:MVPA Notes|MVPA Notes]]
 
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
[[Beauchamp:Electrical Stimulation|Electrical Stimulation]]
#[[Beauchamp:GroupAna|Group Analysis with Unequal Group Sizes using GroupAna.m]]
 
#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
[[Beauchamp:Selectivity|Selectivity]]
#[[Beauchamp:ROIanalysis|ROI Analysis]]


[[Beauchamp:Perceptual Biasing|Perceptual Biasing]]
==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 ]]


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


</div>
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]


==Things to do==
==Electrophysiology/Electrophysiology+MRI==
HumanImageDetection
#[[Beauchamp:Electrode Localization and Naming]]
:Scaling on graphs
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
:Online ranking of top 10 best and top 10 worst stimuli
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
:Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling?
#[[Beauchamp: Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
:Enable online scrambling
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
:Enable online color to black and white conversion
#[[Beauchamp:ActivityMaps|Making Activity Maps]]
Should not reset online display every time you start and stop
#[[Making Resting State Correlation Maps]]
HumanLetterDetection
:Analyze data from LR to see where the RFs are


==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]]


==Things to Order==
==Misc. Experiment Notes==  
staples, stapler
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation  ]
laminator
#[[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]]
#[[Beauchamp:PrintingBrains|How to 3D Print Brains]]

Revision as of 13:11, 20 July 2015

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

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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