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]]
#[[Beauchamp:Autism|Autism Data]]
==Electrophysiology Protocols==


[[Beauchamp:Presurgical Scanning|Presurgical Scanning]]
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Ordering|How To order things for the lab]]


After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles.
==Experimental Design and Analysis==
This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles;
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
  xfiles.hsc.uth.tmc.edu (129.106.148.217)
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
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]]
#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
#[[Beauchamp:MVPA Notes|MVPA Notes]]
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
#[[Beauchamp:GroupAna|Group Analysis with Unequal Group Sizes using GroupAna.m]]
#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
#[[Beauchamp:ROIanalysis|ROI Analysis]]


==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 ]]


<i>In the EMU</i>
==TMS/TMS+MRI==
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]


[[Beauchamp:Setup Apparatus|Setup Apparatus]]
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]


[[Beauchamp:Receptive Field Mapping|Receptive Field Mapping]]
==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]]


[[Beauchamp:Electrical Stimulation|Electrical Stimulation]]
==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:Selectivity|Selectivity]]
==Misc. Experiment Notes==
 
#[[Beauchamp:Stimuli|McGurk Stimuli]]
[[Beauchamp:Perceptual Biasing|Perceptual Biasing]]
#[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]]
 
#[[Beauchamp:Autism|Autism Data]]
It is also good to collect 10 minutes of resting data (no stimulation) from as many visual electrodes as possible for later analyses.
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
</div>
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
 
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
==Things to do==
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
HumanImageDetection
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
:Scaling on graphs
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
:Online ranking of top 10 best and top 10 worst stimuli
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
:Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling?
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
:Enable online scrambling
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
:Enable online color to black and white conversion
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
Should not reset online display every time you start and stop
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]
HumanLetterDetection
:Analyze data from LR to see where the RFs are
Fix labels on amplifier cables (switch a's with b's).
 
 
==Things to Order==
staples, stapler
laminator

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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