Beauchamp:Lab Notebook

From OpenWetWare
Revision as of 07:06, 30 April 2014 by Michael S Beauchamp (talk | contribs) (MRI: fMRI Experimental Design and Analysis)
Brain picture
Beauchamp Lab

General Important Notes

  1. How To Install Software and set up new computers
  2. How To order things for the lab
  3. Information for Subjects and Experimenters, such as Human Subjects Training

MRI: fMRI Experimental Design and Analysis

  1. Overview of fMRI Analysis
  2. How to Collect MRI Data and Use the Scanner
  3. Getting raw data from the scanner
  4. Turning the raw data into AFNI BRIKs
  5. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  6. Motion and Distortion Correction
  7. Creating AFNI BRIKs from MR Data
  8. Creating Volume Average Datasets with AFNI
  9. MVPA Notes
  10. RealTimefMRI
  11. Group Analysis with Unequal Group Sizes using GroupAna.m
  12. HiResolution fMRI
  13. ROI Analysis

MRI: DTI Analysis

  1. Processing Diffusion Tensor Imaging Data
  2. Automatic VOI Initialization for Interactive Tractography
  3. Deterministic Tractography Constrained by Image Masks


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


  1. Eswen Fava's NIRS Manual


  1. Beauchamp:Electrode Localization and Naming
  2. Electrophysiology Protocols
  3. Analyzing ECoG data (by Adam Burch)
  4. Making Resting State Correlation Maps


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

Misc. Experiment Notes

  1. McGurk Stimuli
  2. Autism Data
  3. SR EyeLink Eye Tracker Setup
  4. OLD ASL Eye Tracker Setup
  5. Retinotopic Mapping
  6. AFNI Atlas Values
  7. Tactile Experiment Notes
  8. Notes on analyzing MRI data (old)
  10. HNL Projector Settings
  11. Notes on Stimulus Projector and Screen in UT Philips Scanner
  12. Auditory-only stimuli
  13. Video Stimulus Creation

MRI: Cortical Surface Models

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.

 cd /Volumes/data/UT/IZ/afni

Step 1: Prepare the FreeSurfer directory tree

 /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. This step takes many hours!

 /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 ..

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 ..

For more details, see the following web pages:

  1. Preparation for Creating Cortical Surface Models
  2. Creating Cortical Surface Models
  3. Final touches and using Cortical Surface Models
  4. What If a Cortical Surface Model Exists Already
  5. What If Cortical Surface Model Looks Bad
  6. Creating Standardized Surface Models
  7. FreeSurfer Standard Surface Models
  8. Finding Distances on the Surface
  9. Finding Closest node on the Surface
  10. SUMA
  11. Free Surfer
  12. Caret