Beauchamp:Lab Notebook

From OpenWetWare
Jump to navigationJump to search
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 ExperimentSheet

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. iEEG at BSLMC Workflow
  2. Download iEEG data from
  3. Beauchamp:Electrode Localization and Naming
  4. Electrophysiology Protocols
  5. Analyzing ECoG data (by Adam Burch)
  6. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  7. Clinical Workflow
  8. Electrode Localization using iELVis (by Buffy Nesbitt)
  9. Electrode Localization using steps from the ALICE package
  10. Electrode Localization using steps from the img_pipe package
  11. Analyzing ECoG data (by Muge Ozker Sertel)
  12. Making Activity Maps
  13. Making Resting State Correlation Maps
  14. Using Tobii Eye Tracking Glasses


G Power 3 is a useful program for power analysis

  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

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


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


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

Wordvariability Experiment Notes

  1. Word Stimuli
  2. Transcribe behavioral responses