Beauchamp:Lab Notebook: Difference between revisions

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==MRI==
To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type
#[http://129.106.236.18:8888/mediawiki/index.php/Main_Page UT-Only Wiki]
  site:openwetware.org/wiki/Beauchamp ExperimentSheet
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:Autism|Autism Data]]
==Electrophysiology Protocols==


[[Beauchamp:Presurgical Scanning|Presurgical Scanning]]
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Ordering|How To order things for the lab]]


After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles.
==Experimental Design and Analysis==
This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles;
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
  xfiles.hsc.uth.tmc.edu (129.106.148.217)
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
then the folders can be dragged from the server to Xfiles, or copied in the command line, easily (without using the Web-based GUI interface).
#[[Beauchamp:HowToScan|How to Collect MRI Data and Use the Scanner]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
#[[Beauchamp:CreateAFNIBRIK|Turning the raw data into AFNI BRIKs]]
#[[Beauchamp:CorticalSurfaceOverview|Cortical Surface models overview]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[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:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
#[[Beauchamp:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]


<i>In the EMU</i>
==TMS/TMS+MRI==
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]


[[Beauchamp:Setup Apparatus|Setup Apparatus]]
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]


[[Beauchamp:Receptive Field Mapping|Receptive Field Mapping]]
==Electrophysiology/Electrophysiology+MRI==
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Beauchamp:ECogAnalysisv2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[Making Resting State Correlation Maps]]


[[Beauchamp:Electrical Stimulation|Electrical Stimulation]]
==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:dprime|d' (d-prime) Analysis]]
#[[Beauchamp:RaceModel|Race Model Analysis]]
#[[Beauchamp:100Hue|Stimuli for 100 Hue Experiment]]
#[[Beauchamp:CIMS|Causal Inference model for Synchrony Perception]]
#[[Beauchamp:MCG_Predict|Predicting McGurk Fusion Rates]]


[[Beauchamp:Selectivity|Selectivity]]
==Misc. Experiment Notes==
 
#[[Beauchamp:Stimuli|McGurk Stimuli]]
[[Beauchamp:Perceptual Biasing|Perceptual Biasing]]
#[[Beauchamp:Autism|Autism Data]]
 
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
It is also good to collect 10 minutes of resting data (no stimulation) from as many visual electrodes as possible for later analyses.
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
</div>
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
 
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
After obtaining the CD containing the patient CT data from St. Luke's, use OsiriX to export all images
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
(using the export to DICOM option, and the hierarchical, uncompress options).
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
 
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
CT scans have voxel size 0.488x0.488x1 mm; this may need to be adjusted manually with
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
  3drefit -zdel 1.000 DE_CTSDE+orig
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
(If the CTs look distorted in AFNI, then the voxel size must be adjusted).
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
Next, the CTs must be registered with the hi-res presurgical MRI anatomy.
#[[Beauchamp:VideoStimulusCreation|Video Stimulus Creation]]
This may fail because the CT has a coordinate system with a very different origin than the MRI.
To fix this, type
  3dcopy DE_CTSDE+orig DE_CTSDEshift
  3dinfo DE_CTSDEshift+orig
gives, for example
R-to-L extent:  -124.756 [R] -to-  124.756 [L] -step-    0.488 mm [512 voxels]
A-to-P extent:  -124.756 [A] -to-  124.756 [P] -step-    0.488 mm [512 voxels]
I-to-S extent:  -258.000 [I] -to-  -86.000 [I] -step-    1.000 mm [173 voxels]
 
We want the center of the dataset to be roughly at (0,0,0).
This is true for (x,y) in this case but not for z. We can recenter the z-axis with this command
  3drefit -zorigin 80 DE_CTSDEshift+orig
 
Then, type 3dinfo to check and make sure the z-axis is centered around 0, or examine that MR and the shifted CT
in afni to make sure they are in rough alignment. After they are in rough alignment, use 3dAllineate to align the two datasets.
  3dAllineate -base {$ec}anatavg+orig -source DE_CTSDEshift+orig -prefix {$ec}CTSDE_REGtoanatV4 -verb -warp shift_rotate -cost mutualinfo -1Dfile {$ec}CTSDE_REGtoanatXformV4
 
Again, check in AFNI to make sure that they are aligned. NB: It is also possible to crop the MRI before Allineating since the MR coverage is typically greater than the CT coverage. In a test case, this did not have a big effect.
 
==Things to do==
HumanImageDetection
:Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling? POSSIBLE if original file is vector-based
:Enable online scrambling LOOKING INTO IT
:Enable online color to black and white conversion LOOKING INTO IT
 
HumanLetterDetection
:Analyze data from LR to see where the RFs are
 
==Things to Order==
staples, stapler
laminator

Revision as of 09:03, 14 May 2014

Brain picture
Beauchamp Lab




To search for things on the wiki, use Google's site search feature. For instance, to find an Experiment Sheet, type 

 site:openwetware.org/wiki/Beauchamp ExperimentSheet

General Important Notes

  1. How To Install Software and set up new computers
  2. How To order things for the lab

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. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  8. Motion and Distortion Correction
  9. Creating Volume Average Datasets with AFNI
  10. MVPA Notes
  11. RealTimefMRI
  12. Group Analysis with Unequal Group Sizes using GroupAna.m
  13. HiResolution fMRI
  14. 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. Analyzing ECoG data (by Muge Ozker Sertel)
  5. 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
  13. Video Stimulus Creation
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