Beauchamp:Lab Notebook: Difference between revisions
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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: 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 81: | Line 47: | ||
#[[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| | #[[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]] | ||
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#[[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]] | ||
#[[HNL | #[[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 14:43, 10 January 2014
General Important Notes
- How To Install Software and set up new computers
- How To order things for the lab
- Information for Subjects and Experimenters, such as Human Subjects Training
MRI: fMRI Experimental Design and Analysis
- Getting raw fMRI data from the scanner
- Creating Random Stimulus Orderings For Rapid Event-Related Designs
- Overview of fMRI Analysis
- Motion and Distortion Correction
- Creating AFNI BRIKs from MR Data
- Creating Volume Average Datasets with AFNI
- MVPA Notes
- RealTimefMRI
- Group Analysis with Unequal Group Sizes using GroupAna.m
- HiResolution fMRI
- ROI Analysis
MRI: DTI Analysis
- Processing Diffusion Tensor Imaging Data
- Automatic VOI Initialization for Interactive Tractography
- Deterministic Tractography Constrained by Image Masks
TMS/TMS+MRI
NIRS
Electrophysiology/Electrophysiology+MRI
- Beauchamp:Electrode Localization and Naming
- Electrophysiology Protocols
- Analyzing ECoG data (by Adam Burch)
- 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/
- New Auditory Tactile Experiment
- d' (d-prime) Analysis
- Race Model Analysis
- Stimuli for 100 Hue Experiment
- Causal Inference model for Synchrony Perception
- Predicting McGurk Fusion Rates
Misc. Experiment Notes
- McGurk Stimuli
- Autism Data
- SR EyeLink Eye Tracker Setup
- OLD ASL Eye Tracker Setup
- Retinotopic Mapping
- AFNI Atlas Values
- Tactile Experiment Notes
- Notes on analyzing MRI data (old)
- ANOVAs in MATLAB
- HNL Projector Settings
- Notes on Stimulus Projector and Screen in UT Philips Scanner
- 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:
- Preparation for Creating Cortical Surface Models
- Creating Cortical Surface Models
- Final touches and using Cortical Surface Models
- What If a Cortical Surface Model Exists Already
- What If Cortical Surface Model Looks Bad
- Creating Standardized Surface Models
- FreeSurfer Standard Surface Models
- Finding Distances on the Surface
- Finding Closest node on the Surface
- SUMA
- Free Surfer
- Caret