Beauchamp:Lab Notebook: Difference between revisions
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{{Beauchamp Navigation Bar}} | {{Beauchamp Navigation Bar}} | ||
<br> | <br> | ||
To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type | 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 | 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== | ==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: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]] | |||
==iEEG/ECoG and Related Notes== | |||
#[[Beauchamp:DownloadDataPenn|Download iEEG data from ieeg.org (UPENN data)]] | |||
#[[Beauchamp:Reconstruction and Electrode Labeling (UPenn)|Reconstruction and Electrode Labeling (UPenn)]] | |||
#[[Beauchamp:iEEGWorkflow|iEEG at UPENN-NATUS Workflow]] | |||
#[[Beauchamp:iEEGWorkflow2|iEEG at BCM-EMU Workflow]] | |||
#[[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:ClinicalWorkflow|Clinical Workflow]] | |||
#[[Beauchamp:iELVIS|Electrode Localization using iELVis]] | |||
#[[Beauchamp:ALICE|Electrode Localization using steps from the ALICE package]] | |||
#[[Beauchamp:img_pipe|Electrode Localization using steps from the img_pipe package]] | |||
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]] | |||
#[[Beauchamp:ActivityMaps|Making Activity Maps]] | |||
#[[Making Resting State Correlation Maps]] | |||
#[[Beauchamp:Tobii|Using Tobii Eye Tracking Glasses]] | |||
==RAVE Notes== | |||
#[[Beauchamp:AayushiPreprocessingNotes|RAVE Pre-Processing Pipeline at UPenn (by Aayushi Sangani)]] | |||
==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]] | |||
==Cross Modal Task== | |||
#[[beauchamp: iEEG EMU SOP| 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/ | |||
#[[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:VideoStimulusCreation|Video Stimulus Creation in Premiere]] | |||
==Experimental Design and Analysis== | |||
==fMRI Experimental Design and Analysis== | |||
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]] | #[[Beauchamp:fMRIOverview|Overview of MRI Experiments]] | ||
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]] | #[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]] | ||
Line 18: | Line 70: | ||
#[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]] | #[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]] | ||
#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]] | #[[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:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]] | ||
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | #[[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | ||
#[[Beauchamp:RestingState|Resting State Analysis]] | |||
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]] | #[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]] | ||
#[[Beauchamp:MVPA Notes|MVPA Notes]] | #[[Beauchamp:MVPA Notes|MVPA Notes]] | ||
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#[[Beauchamp:HiResfMRI|HiResolution fMRI]] | #[[Beauchamp:HiResfMRI|HiResolution fMRI]] | ||
#[[Beauchamp:ROIanalysis|ROI Analysis]] | #[[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]] | |||
==MRI: DTI Analysis== | ==MRI: DTI Analysis== | ||
Line 31: | Line 89: | ||
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]] | #[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]] | ||
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]] | #[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]] | ||
#[[Beauchamp:UsingTORTOISE|Using TORTOISE ]] | |||
#[[Beauchamp:VibrationArtifacts|Some approaches for correcting DTI Vibration Artifacts ]] | |||
==TMS/TMS+MRI== | ==TMS/TMS+MRI== | ||
Line 38: | Line 98: | ||
==NIRS== | ==NIRS== | ||
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]] | #[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]] | ||
==Misc. Experiment Notes== | ==Misc. Experiment Notes== | ||
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation ] | |||
#[[Beauchamp:Stimuli|McGurk Stimuli]] | #[[Beauchamp:Stimuli|McGurk Stimuli]] | ||
#[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]] | #[[Beauchamp:LocalizerStimuli|Word Localizer Stimuli]] | ||
Line 70: | Line 114: | ||
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]] | #[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]] | ||
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]] | #[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]] | ||
#[[Beauchamp: | #[[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
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
- Guide for new lab members
- How To Install Software and set up new computers
- How To Install AFNI
- How To order things for the lab
- Sign-up for CAMRI Project Tracking System
iEEG/ECoG and Related Notes
- Download iEEG data from ieeg.org (UPENN data)
- Reconstruction and Electrode Labeling (UPenn)
- iEEG at UPENN-NATUS Workflow
- iEEG at BCM-EMU Workflow
- Beauchamp:Electrode Localization and Naming
- Electrophysiology Protocols
- Analyzing ECoG data (by Adam Burch)
- Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
- Clinical Workflow
- Electrode Localization using iELVis
- Electrode Localization using steps from the ALICE package
- Electrode Localization using steps from the img_pipe package
- Analyzing ECoG data (by Muge Ozker Sertel)
- Making Activity Maps
- Making Resting State Correlation Maps
- Using Tobii Eye Tracking Glasses
RAVE Notes
Noisy Speech Project Experiment Notes
Cross Modal Task
Psychophysics and Stimulus Creation
G Power 3 is a useful program for power analysis http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/
- New Auditory Tactile Experiment
- d' (d-prime) Analysis
- Race Model Analysis
- Stimuli for 100 Hue Experiment
- Causal Inference model for Synchrony Perception
- Predicting McGurk Fusion Rates
- Effect of Video Playback Rate on McGurk Fusion Rates
- Video Stimulus Creation in Premiere
fMRI Experimental Design and Analysis
- Overview of MRI Experiments
- Information for Subjects and Experimenters, such as Human Subjects Training
- How to Collect MRI Data and Use the Scanner
- Getting raw data from the scanner
- Turning the raw data into AFNI BRIKs
- Cortical Surface models overview
- Using the HCP Atlas Area Labels from Glasser et al. in AFNI/SUMA
- Creating Random Stimulus Orderings For Rapid Event-Related Designs
- Motion and Distortion Correction
- Resting State Analysis
- Creating Volume Average Datasets with AFNI
- MVPA Notes
- RealTimefMRI
- Group Analysis with Unequal Group Sizes using GroupAna.m
- HiResolution fMRI
- ROI Analysis
- Drawing ROIs on the cortical surface with SUMA
- Automating AFNI and SUMA
- Finding Release Burst Duration
- Unwarping EPI data
MRI: DTI Analysis
- Processing Diffusion Tensor Imaging Data
- Automatic VOI Initialization for Interactive Tractography
- Deterministic Tractography Constrained by Image Masks
- Using TORTOISE
- Some approaches for correcting DTI Vibration Artifacts
TMS/TMS+MRI
NIRS
Misc. Experiment Notes
- Link to AFNI/SUMA documentation
- McGurk Stimuli
- Word Localizer Stimuli
- Autism Data
- SR EyeLink Eye Tracker Setup
- OLD ASL Eye Tracker Setup
- Retinotopic Mapping
- AFNI Atlas Values
- Tactile Experiment Notes
- Notes on analyzing MRI data (old)
- ANOVAs in MATLAB
- HNL Projector Settings
- Notes on Stimulus Projector and Screen in UT Philips Scanner
- Auditory-only stimuli
- How to 3D Print Brains
- RHOPLS for ECoG Data
- How to make pretty images for participants
- Screencasts of Repeating McGurk Experiments
- Some initial pCASL processing notes using BASIL