mris_make_surfaces
mris_make_surfaces [options] <subject name> <hemisphere>
This program positions the tessellation of the cortical surface at the white matter surface, then the gray matter surface and generate surface files for these surfaces as well as a 'curvature' file for the cortical thickness, and a surface file which approximates layer IV of the cortical sheet.
| Argument | Explanation |
|---|---|
| <Subject Name> | |
| <Hemisphere> | r(right) or l(left) brain hemisphere |
| Argument | Explanation |
|---|---|
| -q | Omit self-intersection and only generate gray/white surface |
| -c | Create curvature and area files from white matter surface |
| -a <avgs> | Average curvature values <avgs> times (default=10) |
| -first_wm_peak | Settle WM surface at first peak in intensity profile instead of highest |
| -whiteonly | Only generate white matter surface |
| -orig_white <surf> | specify a white surface to start with |
| -orig_pial <surf> | specify a pial surface to start with |
| -w <value> | unknown |
| -pa <avgs> | average pial curvature values a max of <avgs> times (default=16) |
| -wa <avgs> | average white curvature values a max of <avgs> times (default=4) |
| -T1 T1vol | default is brain |
| -wvol whitevol <hires> | |
| -long | longitudinal |
| -dura_thresh <threshold> | set a threshold for the multi-echo mprage dura avoidance instead of automatically estimating it |
| -SDIR | SUBJECTS_DIR |
| -pial | pialsurfname |
| -white | whitesurfname |
| -nsigma_above n | # of sigmas above the mean to allow gray matter T2 intensities |
| -nsigma_below n | # of sigmas below the mean to allow gray matter T2 intensities |
Report bugs to <freesurfer@nmr.mgh.harvard.edu>