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://129.106.236.9:8888/mediawiki/index.php/Main_Page Internal Wiki (UTHSC-H Only)]
  site:openwetware.org/wiki/Beauchamp ExperimentSheet
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:Autism|Autism Data]]


==Electrophysiology Protocols==
==General Important Notes==
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:AFNI_Install|How To Install AFNI]]
#[[Beauchamp:Ordering|How To order things for the lab]]
#[[Beauchamp:CAMRI_PTS|Sign-up for CAMRI Project Tracking System]]


[[Beauchamp:Presurgical Scanning|Presurgical Scanning]]
==Experimental Design and Analysis==
#[[Beauchamp:fMRIOverview|Overview of MRI Experiments]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
#[[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]]
#[[Beauchamp:AutomatingAFNI|Automating AFNI and SUMA]]


After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles.
==MRI: DTI Analysis==
This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles;
#[[Beauchamp:ProcessDiffTensImgData|Processing Diffusion Tensor Imaging Data ]]
  xfiles.hsc.uth.tmc.edu (129.106.148.217)
#[[Beauchamp:InitialAutoVOIforIT|Automatic VOI Initialization for Interactive Tractography ]]
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:DetermineTract|Deterministic Tractography Constrained by Image Masks ]]


==TMS/TMS+MRI==
#[[Beauchamp:TMSOverview|Overview of an MRI/fMRI guided TMS Experiment]]
#[[Beauchamp:TMS|Notes on TMS]]


<i>In the EMU</i>
==NIRS==
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]


[[Beauchamp:Setup Apparatus|Setup Apparatus]]
==Electrophysiology/Electrophysiology+MRI==
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Beauchamp: Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)|Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)]]
#[[Beauchamp: ECogAnalysisV2|Analyzing ECoG data (by Muge Ozker Sertel)]]
#[[Beauchamp:ActivityMaps|Making Activity Maps]]
#[[Making Resting State Correlation Maps]]


[[Beauchamp:Receptive Field Mapping|Receptive Field Mapping]]
==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:NED|Predicting McGurk Fusion Rates]]
#[[Beauchamp:Playback Rate|Effect of Video Playback Rate on McGurk Fusion Rates]]


[[Beauchamp:Electrical Stimulation|Electrical Stimulation]]
==Misc. Experiment Notes==
 
#[http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ Link to AFNI/SUMA documentation  ]
[[Beauchamp:Selectivity|Selectivity]]
#[[Beauchamp:Stimuli|McGurk Stimuli]]
 
#[[Beauchamp:LocalizerStimuli|Word Localizer 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.
#[[Beauchamp:PrintingBrains|How to 3D Print Brains]]
Registration routines will not work if the input datasets are not in rough alignment.
To check this, type
  3dinfo DE_CTSDE+orig
returns
  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). For this example, this is true for (x,y) but not for z.
First, create a copy of the dataset
  3dcopy DE_CTSDE+orig DE_CTSDEshift
Then, recenter the z-axis
  3drefit -zorigin 80 DE_CTSDEshift+orig
3dinfo returns
  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:  -80.000 [I] -to-    92.000 [S] -step-    1.000 mm [173 voxels]
 
The z-axis is now roughly centered around 0. In AFNI, examine the MR and the shifted CT to make sure they are in rough alignment. Next, 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
 
Check in AFNI to make sure that they alignment is correct. 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
 
transfer roller for Dell printer
 
==Installing Matlab==
To install Matlab for use in the Beauchamp lab:
:1. Download and install matlab [http://www.mathworks.com/downloads/web_downloads here]. Get login name and pw from Mike
:Note: you will be prompted to install Java run-time environment 5. This will ease the installation.
:2. Place license.dat  in the MATLAB folder when prompted.
:3. Find out that Matlab is already on the computer and cancel installation.

Revision as of 13:38, 14 February 2017

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 Install AFNI
  3. How To order things for the lab
  4. Sign-up for CAMRI Project Tracking System

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
  15. Automating AFNI and SUMA

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. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  5. Analyzing ECoG data (by Muge Ozker Sertel)
  6. Making Activity Maps
  7. 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
  7. Effect of Video Playback Rate on McGurk Fusion Rates

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. Video Stimulus Creation
  16. How to 3D Print Brains
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