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


==Electrophysiology==
==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]]


</div>
==Experimental Design and Analysis==
Typical Protocol
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[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]]


<p>Monday - electrode implantation<br>
==MRI: DTI Analysis==
1. check batteries on BAK stimulator - change if reading lower than 115V (reads ~ 135V with brand new complement of batteries)<br>
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
2. check batteries on patient interface - change if reading lower than 18V (reads ~ 27V with brand new complement of batteries)<br>
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
3. set up cabling for ITC to record from 16 channels (unplug channel 1 to test stimulation circuit) <br>
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
4. using the oscilloscope, check TTL pulse for gate and monitor out signal with stimulation circuit online<br>
5. pick up CT scan from radiology library (signed HIPAA release required) after surgery (~11AM)<br>
6. merge 2nd structural MRI with CT on Stealth<br>
7. merge 2nd structural MRI with CT on AFNI and view with functional activation on cortical surface to select candidate electrodes<br>
8. have Lisa or Rodney jumper the candidate electrodes from the jackbox to our amplifiers<br>
9. double check that the jumpered electrodes are the ones we want<br>
10. make sure cart, display, and eye tracker are room-ready<br>
11. have tape measure, several surgical grounding pads available<br>
</p>


<p>Tuesday or Wednesday - experiments
==TMS/TMS+MRI==
1.
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]


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


==Orders==
==Electrophysiology/Electrophysiology+MRI==
staples
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[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]]
 
==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]]
 
==Misc. Experiment Notes==
#[[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]]

Revision as of 07:34, 30 October 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 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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