brain

Stanford NIRS lab

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...
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...
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...
Xu Cui
42 sec read

recon-all images

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...
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...
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...
Xu Cui
10 min read

Lucas Center tips

Hardware settings In the “Projector source” panel, click “eprime” button to select Eprime as source. Always turn the knob to “SRBox” instead of “USBox”....
Xu Cui
21 sec read

Trigger scanner script: E-Prime and MatLab

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...
Xu Cui
1 min read

xjView, a viewing program for SPM2, SPM5, SPM8 and…

xjView’s official webpage moves to https://www.alivelearn.net/xjview/ xjView is a MatLab program Jian and I wrote a few years ago to display SPM T-test images...
Xu Cui
33 sec read

retinotopy with freesurfer

Retinotopy analysis consists two parts, one on high resolution structural images (segmentation, inflation, cut, etc), the other on...
Xu Cui
2 min read