Beauchamp:Lab Notebook: Difference between revisions

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==General Notes==
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
 
==Notes==
Most important information has migrated to the LabArchives Electronic Research Notebook
  https://mynotebook.labarchives.com/
Visit this website to create an account
  https://researchnotebooks.upenn.edu/getting-started/
When you create your LabArchives account, make sure to use your PennKey@upenn.edu email address, NOT your FirstName.LastName@pennmedicine.upenn.edu address
 
==General Important Notes==
#[[Beauchamp:Orientation|Guide for new lab members]]
#[[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]]


==Subject Forms==
#[[Beauchamp:Subjects|Information for Subjects]]


==MRI==
==iEEG/ECoG and Related Notes==
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
#[[Beauchamp:DownloadDataPenn|Download iEEG data from ieeg.org (UPENN data)]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:Reconstruction and Electrode Labeling (UPenn)|Reconstruction and Electrode Labeling (UPenn)]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:iEEGWorkflow|iEEG at UPENN-NATUS Workflow]]
#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
#[[Beauchamp:iEEGWorkflow2|iEEG at BCM-EMU Workflow]]
#[[Beauchamp:SurfaceMetrics|Finding Closest node on the Surface]]
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
#[[Beauchamp:Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
#[[Beauchamp:UseCortSurfMod|Using Cortical Surface Models]]
#[[Beauchamp:ClinicalWorkflow|Clinical Workflow]]
#[[Beauchamp:IfCortModExists|What If a Cortical Surface Model Exists Already]]
#[[Beauchamp:iELVIS|Electrode Localization using iELVis]]
#[[Beauchamp:EditingCortSurf|What If Cortical Surface Model Looks Bad]]
#[[Beauchamp:ALICE|Electrode Localization using steps from the ALICE package]]
#[[Beauchamp:CreateStndSurfModNew|Creating Standardized Surface Models]]
#[[Beauchamp:img_pipe|Electrode Localization using steps from the img_pipe package]]
#[[Beauchamp:FSStndSurf|FreeSurfer Standard Surface Models]]
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
#[[Beauchamp:ActivityMaps|Making Activity Maps]]
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Making Resting State Correlation Maps]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:Tobii|Using Tobii Eye Tracking Glasses]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
#[[Beauchamp:AFNI|AFNI]]
#[[Beauchamp:SUMA|SUMA]]
#[[Beauchamp:FreeSurfer|Free Surfer]]
#[[Beauchamp:Caret|Caret]]
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
#[[Beauchamp:MVPA Notes|MVPA Notes]]
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
 
==TMS/TMS+MRI==
#[[Beauchamp:TMS|Notes on TMS]]


==RAVE Notes==
#[[Beauchamp:AayushiPreprocessingNotes|RAVE Pre-Processing Pipeline at UPenn (by Aayushi Sangani)]]


==Electrophysiology/Electrophysiology+MRI==
==Noisy Speech Project Experiment Notes==  
#[[Beauchamp:word stimuli|Word Stimuli]]
#[[Beauchamp:transcription|Transcribe behavioral responses]]
#[[Beauchamp:iEEG EMU SOP|Instructions for EMU Patients_SOP]]
#[[Beauchamp:iEEG EMU MATLAB SOP|MATLAB set up_SOP]]


#[[Electrode Localization and Naming]]
==Cross Modal Task==
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[beauchamp: iEEG EMU SOP| Instructions for EMU Patients_SOP (by Aayushi Sangani)]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]


 
==Psychophysics and Stimulus Creation==  
==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:AuditoryTactile|New Auditory Tactile Experiment]]
#[[Beauchamp:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:RaceModel|Race Model 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:VideoStimulusCreation|Video Stimulus Creation in Premiere]]


==Ordering==


==fMRI Experimental Design and Analysis==
#[[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:CorticalSurfaceHCP|Using the HCP Atlas Area Labels from Glasser et al. in AFNI/SUMA]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:RestingState|Resting State Analysis]]
#[[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:DrawingROIs|Drawing ROIs on the cortical surface with SUMA]]
#[[Beauchamp:AutomatingAFNI|Automating AFNI and SUMA]]
#[[Finding Release Burst Duration]]
#[[Beauchamp:Unwarping|Unwarping EPI data]]


==McGurk Stimuli==  
==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 ]]
#[[Beauchamp:UsingTORTOISE|Using TORTOISE ]]
#[[Beauchamp:VibrationArtifacts|Some approaches for correcting DTI Vibration Artifacts ]]


[[Beauchamp:Stimuli|McGurk Stimuli]]
==TMS/TMS+MRI==
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]
 
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]
 
==Misc. Experiment Notes==
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation  ]
#[[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:PrintingBrains|How to 3D Print Brains]]
#[[Beauchamp:TensorECOG|RHOPLS for ECoG Data]]
#[[Beauchamp:BrainPix|How to make pretty images for participants]]
#[[Screencasts of Repeating McGurk Experiments]]
#[[Some initial pCASL processing notes using BASIL]]

Latest revision as of 10:30, 21 July 2023

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

Notes

Most important information has migrated to the LabArchives Electronic Research Notebook 

 https://mynotebook.labarchives.com/

Visit this website to create an account 

 https://researchnotebooks.upenn.edu/getting-started/

When you create your LabArchives account, make sure to use your PennKey@upenn.edu email address, NOT your FirstName.LastName@pennmedicine.upenn.edu address

General Important Notes

  1. Guide for new lab members
  2. How To Install Software and set up new computers
  3. How To Install AFNI
  4. How To order things for the lab
  5. Sign-up for CAMRI Project Tracking System


iEEG/ECoG and Related Notes

  1. Download iEEG data from ieeg.org (UPENN data)
  2. Reconstruction and Electrode Labeling (UPenn)
  3. iEEG at UPENN-NATUS Workflow
  4. iEEG at BCM-EMU Workflow
  5. Beauchamp:Electrode Localization and Naming
  6. Electrophysiology Protocols
  7. Analyzing ECoG data (by Adam Burch)
  8. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  9. Clinical Workflow
  10. Electrode Localization using iELVis
  11. Electrode Localization using steps from the ALICE package
  12. Electrode Localization using steps from the img_pipe package
  13. Analyzing ECoG data (by Muge Ozker Sertel)
  14. Making Activity Maps
  15. Making Resting State Correlation Maps
  16. Using Tobii Eye Tracking Glasses

RAVE Notes

  1. RAVE Pre-Processing Pipeline at UPenn (by Aayushi Sangani)

Noisy Speech Project Experiment Notes

  1. Word Stimuli
  2. Transcribe behavioral responses
  3. Instructions for EMU Patients_SOP
  4. MATLAB set up_SOP

Cross Modal Task

  1. Instructions for EMU Patients_SOP (by Aayushi Sangani)

Psychophysics and Stimulus Creation

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
  8. Video Stimulus Creation in Premiere


fMRI 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. Using the HCP Atlas Area Labels from Glasser et al. in AFNI/SUMA
  8. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  9. Motion and Distortion Correction
  10. Resting State Analysis
  11. Creating Volume Average Datasets with AFNI
  12. MVPA Notes
  13. RealTimefMRI
  14. Group Analysis with Unequal Group Sizes using GroupAna.m
  15. HiResolution fMRI
  16. ROI Analysis
  17. Drawing ROIs on the cortical surface with SUMA
  18. Automating AFNI and SUMA
  19. Finding Release Burst Duration
  20. Unwarping EPI data

MRI: DTI Analysis

  1. Processing Diffusion Tensor Imaging Data
  2. Automatic VOI Initialization for Interactive Tractography
  3. Deterministic Tractography Constrained by Image Masks
  4. Using TORTOISE
  5. Some approaches for correcting DTI Vibration Artifacts

TMS/TMS+MRI

  1. Overview of an MRI/fMRI guided TMS Experiment
  2. Notes on TMS

NIRS

  1. Eswen Fava's NIRS Manual

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. How to 3D Print Brains
  16. RHOPLS for ECoG Data
  17. How to make pretty images for participants
  18. Screencasts of Repeating McGurk Experiments
  19. Some initial pCASL processing notes using BASIL
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