brain
convert between different image formats strip skull (FSL bet, or Bet for gui) bet brain.nii brain_noskull.nii register to a standard brain (FSL flirt, or Flirt for gui) Select avg152T1_brain.img as reference, use rigid body (6 parameters) A mat file
Check out Near infrared spectroscopy (NIRS) Lab I take charge of: http://spnl.stanford.edu/tools/nirsCIBSR/nirsHome.htm NIRS allows you to measure neural activities on the surface of the brain. Some labs use NIRS to do brain-computer interface, i.e.
Below are some pictures of my own brain. 001 rawavg orig nu T1 brainmask norm nu_noneck aseg brain brain.finalsurfs wm.seg wm filled lh.orig.nofix lh.smoothwm.nofix lh.inflated.nofix lh.qsphere.nofix lh.orig lh.white lh.pial lh.smoothwm lh.inflated l
ROI stands for region of interest. The region is predefined usually from glm contrast. For example, you find visual cortex is activated when a flash is presented through glm analysis, you may then do more analysis on this particular region. ROI analy
Check out recon-all procedures here rawavg orig nu T1 brainmask norm nu_noneck aseg.auto aseg.auto_noCCseg aseg brain wm.seg filled lh.orig lh.smoothwm lh.inflated.nofix lh.qsphere.nofix lh.white lh.pial lh.inflated lh.sphere
Assume CON14 is our subject ID and it is inside directory $SUBJECTS_DIR. After the display window and the control panel pops up, try playing with the menus and buttons. tkmedit for volume tkmedit CON14 rawavg.mgz tkmedit CON14 rawavg.mgz lh.pial -aux
recon-all is a batch program and runs >30 steps. It easily takes 30 hours to finish one subject. Use tkmedit CON14 T1.mgz and tksurfer CON14 lh inflated to visualize images. More about visualization with freesurfer. Note: commands are in green. T
Hardware settings In the “Projector source” panel, click “eprime” button to select Eprime as source. Always turn the knob to “SRBox” instead of “USBox”. Transfering data: You use gFTP to transfer data f
E-Prime This piece of code is used in Lucas Center scanner #2 at Stanford University. SRBOX.Lamps "4" Sleep(100) SRBOX.Lamps "" Set SumACC = New Summation You also need to declare SumACC in user script Dim SumACC = As Summation Ma
