Beauchamp:Lab Notebook: Difference between revisions
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==MRI: Cortical Surface Models== | ==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. | 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 | cd /Volumes/data1/UT/IZ/afni | ||
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/Volumes/data1/UT/scripts/@prep_dir IZanatavg+orig.BRIK | /Volumes/data1/UT/scripts/@prep_dir IZanatavg+orig.BRIK | ||
Step 2: Reconstruct the surface. Note that no argument is required, but if you are using the up arrow to recall the last command and edit it, there is no need to remove the argument. | Step 2: Reconstruct the surface. Note that no argument is required, but if you are using the up arrow to recall the last command and edit it, there is no need to remove the argument. | ||
/Volumes/data1/scripts/@recon IZanatavg+orig.BRIK | /Volumes/data1/scripts/@recon IZanatavg+orig.BRIK | ||
Step 3: Finish the surface | Step 3: Finish the surface | ||
/Volumes/data1/scripts/@finish IZanatavg+orig.BRIK | /Volumes/data1/scripts/@finish IZanatavg+orig.BRIK | ||
For more details, see the following web pages: | For more details, see the following web pages: | ||
#[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]] | #[[Beauchamp:PrepCortSurfModels|Preparation for Creating Cortical Surface Models]] |
Revision as of 07:28, 27 September 2011
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: 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/UT/scripts/@prep_dir IZanatavg+orig.BRIK
Step 2: Reconstruct the surface. Note that no argument is required, but if you are using the up arrow to recall the last command and edit it, there is no need to remove the argument.
/Volumes/data1/scripts/@recon IZanatavg+orig.BRIK
Step 3: Finish the surface
/Volumes/data1/scripts/@finish IZanatavg+orig.BRIK
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
MRI: fMRI Experimental Design and Analysis
- 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
- Electrode Localization and Naming
- Electrophysiology Protocols
- Analyzing ECoG data (by Adam Burch)
- Making Resting State Correlation Maps
Psychophysics
- New Auditory Tactile Experiment
- d' (d-prime) Analysis
- Race Model Analysis
- Stimuli for 100 Hue Experiment