Beauchamp

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Beauchamp Lab wiki



Thank you for visiting the Beauchamp Lab wiki, for a more aesthetically appealing (and official UPenn) site, visit:

Click here for the Beauchamp Lab website at the University of Pennsylvania

Some items that may be helpful:

  1. PDFs of all Beauchamp Lab publications
  2. Resources, include stimuli and code from publications
  3. Older version of lab notebook links, newer version below

Click here for the Research Division of the Department of Neurosurgery at the University of Pennsylvania

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 for Beauchamp Lab members

there is an instructions manual for new lab members in at https://www.dropbox.com/work/BeauchampLabAtPenn/SOP

Private lab 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


Penn uses a 26 digit number for funding sources that is broken into segments that mean something. More info about the setup is available here - https://provost.upenn.edu/wp-content/uploads/BEN-Budget-Code-Explanation.pdf Your CNAC will usually be 400 (School of Medicine, org 4504 (Neurosurgery), prog 2810 (Neuroscience) and cref 4919 (Beauchamp). The BC (budget check) depends on the kind of funding and the funding is a 6 digit assigned to the grant, gift, endowment, or department fund.

Richards 6A Brother MFC (printer)

On Mac OSX, go to Settings/Printers. Click the "+" button to add a printer, click on the globe icon (for web/IP) and enter the IP address, currently 

 10.103.203.8

AirPrint protocol (default) is fine.


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. Visit the RAVE website for the most up-to-date information on RAVE
  2. 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. How To Install AFNI
  2. Overview of MRI Experiments
  3. Information for Subjects and Experimenters, such as Human Subjects Training
  4. How to Collect MRI Data and Use the Scanner
  5. Getting raw data from the scanner
  6. Turning the raw data into AFNI BRIKs
  7. Cortical Surface models overview
  8. Using the HCP Atlas Area Labels from Glasser et al. in AFNI/SUMA
  9. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  10. Motion and Distortion Correction
  11. Resting State Analysis
  12. Creating Volume Average Datasets with AFNI
  13. MVPA Notes
  14. RealTimefMRI
  15. Group Analysis with Unequal Group Sizes using GroupAna.m
  16. HiResolution fMRI
  17. ROI Analysis
  18. Drawing ROIs on the cortical surface with SUMA
  19. Automating AFNI and SUMA
  20. Finding Release Burst Duration
  21. 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


Archival Wiki Pages

  1. Old Teaching Notes
  2. Positions
  3. People/Projects/Media
  4. Lab Notebook

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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