Talk by Frans de Waal

Today I listened to Frans de Waal’s talk on empathy in primates. It’s quite interesting. He wrote several popular books including “Chimpanzee Politics”. Links: Frans de Waal
Xu Cui
5 sec read

Analyze NIRS data with NIRS-SPM

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
Xu Cui
4 min read

brain image preprocessing

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
Xu Cui
19 sec read

Stanford NIRS lab

Check out Near infrared spectroscopy (NIRS) Lab I take charge of: NIRS allows you to measure neural activities on the surface of the brain. Some labs use NIRS to do brain-computer interface, i.e.
Xu Cui
11 sec read

My brain in many flavors

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
Xu Cui
11 sec read

fMRI: how to do ROI analysis

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
Xu Cui
42 sec read

recon-all images

Check out recon-all procedures here rawavg orig nu T1 brainmask norm nu_noneck 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
Xu Cui
8 sec read

Visualization with freesurfer

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
Xu Cui
21 sec read

recon-all of freesurfer

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
Xu Cui
10 min read