brain
being updated for v01_r14 … NIRS-SPM is a SPM5 and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals, developed at the Bio Imaging Signal Processing (BISP) lab. at KAIST in Korea. prepare files
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
