Beauchamp:Lab Notebook

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(Misc. Experiment Notes)
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#[[Beauchamp:Ordering|How To order things for the lab]]
#[[Beauchamp:Ordering|How To order things for the lab]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
-
 
-
==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/data1/UT/IZ/afni
 
-
Step 1: Prepare the FreeSurfer directory tree
 
-
  /Volumes/data1/UT/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/data1/scripts/@recon IZanatavg+orig.BRIK
 
-
Step 3: Finish the surface
 
-
  /Volumes/data1/scripts/@finish IZanatavg+orig.BRIK
 
-
Or in a more economical way:
 
-
  set ec = IZ
 
-
  cd /Volumes/data1/UT/{$ec}/afni
 
-
  /Volumes/data1/UT/scripts/@prep_dir {$ec}anatavg+orig.BRIK 
 
-
  /Volumes/data1/scripts/@recon {$ec}anatavg+orig.BRIK
 
-
  /Volumes/data1/scripts/@finish {$ec}anatavg+orig.BRIK
 
-
 
-
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]]
 
==MRI: fMRI Experimental Design and Analysis==
==MRI: fMRI Experimental Design and Analysis==
 +
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw fMRI data from the scanner]]
#[[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:fMRIOverview|Overview of fMRI Analysis]]
Line 64: Line 35:
==Electrophysiology/Electrophysiology+MRI==
==Electrophysiology/Electrophysiology+MRI==
-
#[[Electrode Localization and Naming]]
+
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
Line 70: Line 41:
==Psychophysics==  
==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:AuditoryTactile|New Auditory Tactile Experiment]]
#[[Beauchamp:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:RaceModel|Race Model Analysis]]
#[[Beauchamp:RaceModel|Race Model Analysis]]
#[[Beauchamp:100Hue|Stimuli for 100 Hue Experiment]]
#[[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==  
#[[Beauchamp:Stimuli|McGurk Stimuli]]
#[[Beauchamp:Stimuli|McGurk 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 84: Line 60:
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
 +
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
 +
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
 +
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
 +
 +
==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.
 +
  /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]]

Revision as of 17:43, 10 January 2014

Brain picture
Beauchamp Lab



Contents

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

TMS/TMS+MRI

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

NIRS

  1. Eswen Fava's NIRS Manual

Electrophysiology/Electrophysiology+MRI

  1. Beauchamp:Electrode Localization and Naming
  2. Electrophysiology Protocols
  3. Analyzing ECoG data (by Adam Burch)
  4. 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/

  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)
  9. ANOVAs in MATLAB
  10. HNL Projector Settings
  11. Notes on Stimulus Projector and Screen in UT Philips Scanner
  12. Auditory-only stimuli

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.

 /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:

  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
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