Index

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.

See Also

Links

FreeSurfer, FsFast

Reporting Bugs

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

Author/s

DougGreve, BruceFischl