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

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

retinotopy with freesurfer

Retinotopy analysis consists two parts, one on high resolution structural images (segmentation, inflation, cut, etc), the other on functional images. structural Before you start, you need to put the structural i
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 or MRICro. Here are some special cases: multiple 3D ANALYZE to a single 4D Nifti: mri_conc
Xu Cui
1 min read