brain

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

brain images: convert between different formats

For single file to single file conversion, you usually use mri_convert of freesurfer. For example mri_convert x.img y.nii Other options would be LONI Debabeler...
Xu Cui
1 min read

fslmerge: convert 3D ANALYZE to Nifti

/fs/quarry/cuixu/fsl/fslmerge -t f I_???.* On my computer, it doesn’t convert to .nii file; but to a single img/hdr pair. This method won’t be used....
Xu Cui
8 sec read