freesurfer
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...
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...
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...
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...
Retinotopy analysis consists two parts, one on high resolution structural images (segmentation, inflation, cut, etc), the other on...
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...