Table of Contents
Sam's Scribbles
At some point I would like to streamline all commands into one comprehensive script.
Analysis Commands
Generating ahl gmpva and pva classification performance by voxel number: samnewclassdefault (samneclassdefault9 for s007)
Batch resampling and analyzing data can be run from: samBatchResAnal (look inside this script for subscripts used).
samBatchResAnalhi is used for hi pass data.
One of the subscripts - samresampleclass is run as samresampleclassinf for all voxels to be used for classification.
Generating mean plot of resampled data: samplotresampleaverages
samplotaverages - generates mean.mat - with means for 3 roi types / sems / stds
sammeansplot - plots mean.mat info
Retinotopy
Two methods - BC retino which includes venogram or standard retinotopy by volume coil. Protocols for both can be found in gru svn repository.
Venogram Overlay
Written a script (needs cleanup) to generate overlay from venogram.
doGRUoverlay
This will take 'veno.img' and produce a overlay named 'venoOVER.img' with intensities from 0-1. It will also convert the venogram into 4 dimensions so it can be opened in mrLoadRet. The overlay will be placed in Raw/TSeries. It will ask you to enter details for mrinit and open mralign so that you may align the venogram and session 3d to the canonical. Finally it will load the overlay in mrloadret.
Draw ROIs
Using venogram draw ROIs of veins likely to be in V1 on flatmaps - validate veins by cross referencing between anatomical images and flatmaps.
Reslice
After deciding on target vein load anatomy and ROIs in Reslice and create 3 slice (1 slice is 2mm thick), slice plan.
VT dots
Perform experiment