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'''Index''' <<TableOfContents>>

= Name =
mris_make_surfaces

= Description =
Generates surface files for cortical and white matter surfaces, curvature file for cortical thickness and surface file estimate for layer IV of cortical sheet. 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.

= Synopsis =
mris_make_surfaces [options] <subject name> <hemisphere>

= Arguments =
== Positional Arguments ==
||Subject Name || ||
||Hemisphere ||r(right) or l(left) brain hemisphere ||


== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
||-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) ||
||-whiteonly ||Only generate white matter surface ||
||-orig_white <surf> ||Specify a white surface to start with ||
||-orig_pial <surf> ||Specify a white surface to start with ||
||-w <value> || ||
||-max_gray_scale mgs || In white deformation set outside_hi = (max_border_white + mgs*max_gray) / (mgs+1.0) ||
||-first_wm_peak || Settle WM surface at first peak in intensity profile instead of highest ||
||-pa <avgs> || Average pial curvature values a max of <avgs> times. Default is 16. ||
||-wa <avgs> || Average white curvature values a max of <avgs> times. Default is 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 || Pial surface name ||
||-white || White surface name ||
||-wm_weight w || Weighting of wm mean in calculating T2  threshold of diallowed gm values (w*wm+gm)/(w+1). Default is 3. ||
||-nsigma_above n || Number of sigmas above the mean to allow gray matter T2 intensities. ||
||-nsigma_below n || Number of sigmas below the mean to allow gray matter T2 intensities. ||
||-T2_min threshold || Specify threshold for min T2 values allowed to be interior to the cortical ribbon. ||
||-T2_max threshold || Specify threshold for max T2 values allowed to be interior to the cortical ribbon. ||
||-min_peak_pct inside_pct outside_pct || Specify the pct of the histo peak in the local gm histogram to use as threshold for finding the local inside and outside gm thresholds. Smaller values will cause more intensities to be included as gm. ||
||-help || Prints out help information ||
||-all-info || Prints out full version information ||


= Examples =
== Example 1 ==
{{{
mris_make_surfaces 099 rh
}}}
This command creates the right hemisphere white, pial, and thickness surfaces for subject 099. These surfaces are saved to SUBJECTS_DIR/099/surf. 

= Links =
FreeSurfer, FsFast

= Reporting Bugs =
Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >

= Author/s =
DougGreve, BruceFischl