Beauchamp:Lab Notebook: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
(168 intermediate revisions by 16 users not shown)
Line 3: Line 3:
<div style="padding: 8px; color: #000000; background-color: #ffffff; width: 730px; border: 2px solid #666666;">
<div style="padding: 8px; color: #000000; background-color: #ffffff; width: 730px; border: 2px solid #666666;">


==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: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]]


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]]
#[[Beauchamp:AutomatingAFNI|Automating AFNI and SUMA]]


==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: Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
#[[Beauchamp:ALICE|Electrode Localization using steps from the ALICE package]]
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[Beauchamp:ActivityMaps|Making Activity Maps]]
#[[Making Resting State Correlation Maps]]
#[[Beauchamp:TensorECOG|Tensor Analysis of ECOG data]]
#[[Beauchamp:Tobii|Using Tobii Eye Tracking Glasses]]


[[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:Playback Rate|Effect of Video Playback Rate on McGurk Fusion Rates]]


[[Beauchamp:Selectivity|Selectivity]]
==Misc. Experiment Notes==
 
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation  ]
[[Beauchamp:Perceptual Biasing|Perceptual Biasing]]
#[[Beauchamp:Stimuli|McGurk Stimuli]]
 
#[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]]
It is also good to collect 10 minutes of resting data (no stimulation) from as many visual electrodes as possible for later analyses.
#[[Beauchamp:Autism|Autism Data]]
</div>
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
 
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
==Things to do==
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
HumanImageDetection
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
:Scaling on graphs
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
:Online ranking of top 10 best and top 10 worst stimuli
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
:Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling?
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
:Enable online scrambling
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
:Enable online color to black and white conversion
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
Should not reset online display every time you start and stop
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
HumanLetterDetection
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]
:Analyze data from LR to see where the RFs are
#[[Beauchamp:PrintingBrains|How to 3D Print Brains]]
Fix labels on amplifier cables (switch a's with b's).
#[[Beauchamp:TensorECOG|RHOPLS for ECoG Data]]
 
 
==Things to Order==
staples, stapler
laminator

Revision as of 09:28, 24 July 2017

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
  15. Automating AFNI and SUMA

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. Electrode Localization using steps from the ALICE package
  6. Analyzing ECoG data (by Muge Ozker Sertel)
  7. Making Activity Maps
  8. Making Resting State Correlation Maps
  9. Tensor Analysis of ECOG data
  10. Using Tobii Eye Tracking Glasses

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
  17. RHOPLS for ECoG Data
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Beauchamp:Lab_Notebook&oldid=989895"