Lab Notebook

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Notes

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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

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