Beauchamp:Lab Notebook: Difference between revisions

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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==
==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]]
==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]]
==fMRI Experimental Design and Analysis==
#[[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]]
 
#[[Beauchamp:HowToScan|How to Collect MRI Data and Use the Scanner]]
==MRI: fMRI Experimental Design and Analysis==
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw fMRI 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:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
#[[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==
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#[[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 32: Line 98:
==NIRS==
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]
==Electrophysiology/Electrophysiology+MRI==
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[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:MCG_Predict|Predicting McGurk Fusion Rates]]


==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:Autism|Autism Data]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
Line 62: 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:PrintingBrains|How to 3D Print Brains]]
==MRI: Cortical Surface Models==
#[[Beauchamp:TensorECOG|RHOPLS for ECoG Data]]
There is a simple three step process for creating surface models. The steps assume that you are in the afni subdirectory of the subject for which a surface is to be created.
#[[Beauchamp:BrainPix|How to make pretty images for participants]]
  cd /Volumes/data/UT/IZ/afni
#[[Screencasts of Repeating McGurk Experiments]]
Step 1: Prepare the FreeSurfer directory tree
#[[Some initial pCASL processing notes using BASIL]]
  /Volumes/data/scripts/@prep_dir IZanatavg+orig.BRIK 
Step 2: Reconstruct the surface. Note that the name of the anatomy is not needed, but if you are using the up arrow in the UNIX shell to recall the last command and edit it, there is no need to delete the filename.
  /Volumes/data/scripts/@recon IZanatavg+orig.BRIK
Step 3: Finish the surface
  /Volumes/data/scripts/@finish IZanatavg+orig.BRIK
step 4: Check the created surface
  cd ..
  ./@ec
Or in a more economical way:
  set ec = IZ
  cd /Volumes/data/UT/{$ec}/afni
  /Volumes/data/scripts/@prep_dir {$ec}anatavg+orig.BRIK 
  /Volumes/data/scripts/@recon {$ec}anatavg+orig.BRIK
  /Volumes/data/scripts/@finish {$ec}anatavg+orig.BRIK
  cd ..
  ./@ec
 
For more details, see the following web pages:
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
#[[Beauchamp:UseCortSurfMod|Final touches and using Cortical Surface Models]]
#[[Beauchamp:IfCortModExists|What If a Cortical Surface Model Exists Already]]
#[[Beauchamp:EditingCortSurf|What If Cortical Surface Model Looks Bad]]
#[[Beauchamp:CreateStndSurfModNew|Creating Standardized Surface Models]]
#[[Beauchamp:FSStndSurf|FreeSurfer Standard Surface Models]]
#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
#[[Beauchamp:SurfaceMetrics|Finding Closest node on the Surface]]
#[[Beauchamp:SUMA|SUMA]]
#[[Beauchamp:FreeSurfer|Free Surfer]]
#[[Beauchamp:Caret|Caret]]

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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