Beauchamp:Lab Notebook: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(119 intermediate revisions by 12 users not shown)
Line 3: Line 3:
<div style="padding: 8px; color: #000000; background-color: #ffffff; width: 730px; border: 2px solid #666666;">
<div style="padding: 8px; color: #000000; background-color: #ffffff; width: 730px; border: 2px solid #666666;">


==MRI==
==General Important Notes==
#[http://129.106.236.9:8888/mediawiki/index.php/Main_Page Internal Wiki (UTHSC-H Only)]
#[[Beauchamp:Software_Installation|How To Install Software and set up new computers]]
#[[Beauchamp:Ordering|How To order things for the lab]]
#[[Beauchamp:Subjects|Information for Subjects and Experimenters, such as Human Subjects Training]]
 
==MRI: fMRI Experimental Design and Analysis==
#[[Beauchamp:fMRIOverview|Overview of fMRI Analysis]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw fMRI data from the scanner]]
#[[Beauchamp:RandomStimulus|Creating Random Stimulus Orderings For Rapid Event-Related Designs]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:MotionCorrection|Motion and Distortion Correction]]
#[[Beauchamp:Autism|Autism Data]]
#[[Beauchamp:CreateAFNIBRIKfromMR|Creating AFNI BRIKs from MR Data ]]
#[[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]]


==Electrophysiology Protocols==
==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 ]]


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


After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles.
==NIRS==
This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles;
#[[Beauchamp:NIRS|Eswen Fava's NIRS Manual]]
  xfiles.hsc.uth.tmc.edu (129.106.148.217)
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).


==Electrophysiology/Electrophysiology+MRI==


<i>In the EMU</i>
#[[Beauchamp:Electrode Localization and Naming]]
#[[Beauchamp:Electrophysiology|Electrophysiology Protocols]]
#[[Beauchamp:ECogAnalysis|Analyzing ECoG data (by Adam Burch)]]
#[[Making Resting State Correlation Maps]]


[[Beauchamp:Setup Apparatus|Setup Apparatus]]
==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:Receptive Field Mapping|Receptive Field Mapping]]
==Misc. Experiment Notes==
 
#[[Beauchamp:Stimuli|McGurk Stimuli]]
[[Beauchamp:Electrical Stimulation|Electrical Stimulation]]
#[[Beauchamp:Autism|Autism Data]]
 
#[[Beauchamp:NewEyeTrackSetup|SR EyeLink Eye Tracker Setup]]
[[Beauchamp:Selectivity|Selectivity]]
#[[Beauchamp:EyeTrackSetup|OLD ASL Eye Tracker Setup]]
 
#[[Beauchamp:Retinotopy|Retinotopic Mapping ]]
[[Beauchamp:Perceptual Biasing|Perceptual Biasing]]
#[[Beauchamp:ZillesAtlasValues|AFNI Atlas Values]]
 
#[[Beauchamp:Tactile_Experiment_Notes|Tactile Experiment Notes]]
It is also good to collect 10 minutes of resting data (no stimulation) from as many visual electrodes as possible for later analyses.
#[[Beauchamp:MRI_Data_Analysis|Notes on analyzing MRI data (old)]]
</div>
#[[Beauchamp:ANOVAs in MATLAB|ANOVAs in MATLAB]]
 
#[[Media:Beauchamp-Projector_settings.pdf|HNL Projector Settings]]
After obtaining the CD containing the patient CT data from St. Luke's, use OsiriX to export all images
#[[Beauchamp:ProjectionNotes|Notes on Stimulus Projector and Screen in UT Philips Scanner]]
(using the export to DICOM option, and the hierarchical, uncompress options).
#[[Beauchamp:Unisensory Stimuli|Auditory-only stimuli]]
 
CT scans have voxel size 0.488x0.488x1 mm; this may need to be adjusted manually with
  3drefit -zdel 1.000 DE_CTSDE+orig
(If the CTs look distorted in AFNI, then the voxel size must be adjusted).
Next, the CTs must be registered with the hi-res presurgical MRI anatomy.
This may fail because the CT has a coordinate system with a very different origin than the MRI.
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
==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


transfer roller for Dell printer
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 07:50, 17 April 2014

Brain picture
Beauchamp Lab




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. Overview of fMRI Analysis
  2. Getting raw fMRI data from the scanner
  3. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  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
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Beauchamp:Lab_Notebook&oldid=788760"