Beauchamp:Lab Notebook

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-
==General Notes==
+
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[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]]
-
==Subject Forms==
+
==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]]
-
==MRI==
+
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
-
#[[Beauchamp:Software_Installation|Software Information Page]]
 
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
-
#[[Beauchamp:Autism|Autism Data]]
 
-
#[[Beauchamp:SurfDist|Finding Distances on the Surface]]
 
-
#[[Beauchamp:SurfaceMetrics|Finding Closest node on the Surface]]
 
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
-
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
 
-
#[[Beauchamp:CreateCortSurfMod|Creating Cortical Surface Models]]
 
-
#[[Beauchamp:UseCortSurfMod|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:VolAverage|Creating Volume Average Datasets with AFNI]]
#[[Beauchamp:VolAverage|Creating Volume Average Datasets with AFNI]]
 +
#[[Beauchamp:MVPA Notes|MVPA Notes]]
 +
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
 +
#[[Beauchamp:GroupAna|Group Analysis with Unequal Group Sizes using GroupAna.m]]
 +
#[[Beauchamp:HiResfMRI|HiResolution fMRI]]
 +
#[[Beauchamp:ROIanalysis|ROI Analysis]]
 +
 +
==MRI: DTI Analysis==
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]
-
#[[Beauchamp:AFNI|AFNI]]
 
-
#[[Beauchamp:SUMA|SUMA]]
 
-
#[[Beauchamp:FreeSurfer|Free Surfer]]
 
-
#[[Beauchamp:Caret|Caret]]
 
-
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
 
-
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
 
-
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
 
-
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
 
-
#[[Beauchamp:MVPA Notes|MVPA Notes]]
 
-
#[[Beauchamp:RealTimefMRI|RealTimefMRI]]
 
-
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
 
==TMS/TMS+MRI==
==TMS/TMS+MRI==
 +
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]
#[[Beauchamp:TMS|Notes on TMS]]
 +
==NIRS==
 +
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]
==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)]]
-
 
+
#[[Making Resting State Correlation Maps]]
==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]]
-
==Ordering==  
+
==Misc. Experiment Notes==  
 +
#[[Beauchamp:Stimuli|McGurk Stimuli]]
 +
#[[Beauchamp:Autism|Autism Data]]
 +
#[[Beauchamp:EyeTrackSetup|Scanner Stimulus and Eye Tracker Setup]]
 +
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
 +
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
 +
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
 +
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
 +
#[[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]]
 +
==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/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
 +
step 4: Check the created surface
 +
  cd ..
 +
  ./@ec
 +
Or in a more economical way:
 +
  set ec = IZ
 +
  cd /Volumes/data1/UT/{$ec}/afni
 +
  /Volumes/data1/scripts/@prep_dir {$ec}anatavg+orig.BRIK 
 +
  /Volumes/data1/scripts/@recon {$ec}anatavg+orig.BRIK
 +
  /Volumes/data1/scripts/@finish {$ec}anatavg+orig.BRIK
 +
  cd ..
 +
  ./@ec
-
==McGurk Stimuli==
+
For more details, see the following web pages:
-
 
+
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]]
-
[[Beauchamp:Stimuli|McGurk Stimuli]]
+
#[[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 10:23, 24 August 2012

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

Misc. Experiment Notes

  1. McGurk Stimuli
  2. Autism Data
  3. Scanner Stimulus and Eye Tracker Setup
  4. Retinotopic Mapping
  5. AFNI Atlas Values
  6. Tactile Experiment Notes
  7. Notes on analyzing MRI data (old)
  8. ANOVAs in MATLAB
  9. HNL Projector Settings
  10. Notes on Stimulus Projector and Screen in UT Philips Scanner

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/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

step 4: Check the created surface

 cd ..
 ./@ec

Or in a more economical way:

 set ec = IZ
 cd /Volumes/data1/UT/{$ec}/afni
 /Volumes/data1/scripts/@prep_dir {$ec}anatavg+orig.BRIK  
 /Volumes/data1/scripts/@recon {$ec}anatavg+orig.BRIK
 /Volumes/data1/scripts/@finish {$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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