'''Index'''
<<TableOfContents>>
= Name =
pctsurfcon - Computes surface-wise gray/white contrast.
= Synopsis =
pctsurfcon --s subjid
= Arguments =
== Required Flagged Arguments ==
|| --s subject || FreeSurfer subject name ||

== Optional Flagged Arguments ==
|| --fsvol fsvol || use fsvol instead of rawavg ||
|| --b outbase || use outbase instead of w-g.pct (?h.w-g.pct.mgh) ||
|| --lh-only, --no-rh || compute left hemisphere only ||
|| --rh-only, --no-lh || compute right hemisphere only ||
|| --gm-proj-frac frac || GM projection fraction (default, 0.3) ||
|| --gm-proj-abs dist || GM projection distance (default is to use frac) ||
|| --wm-proj-abs dist || WM projection distance (default is 1mm) ||
|| --neg || Compute G-W instead of W-G ||
|| --no-mask || Do not mask out non-cortical regions ||
|| --tmp tmpdir || Temporary dir (implies --nocleanup) ||
|| --nocleanup || Do not delete temporary files ||
|| --version || Print version and exit ||
|| --help || Print help and exit ||

= Outputs =
|| <subjid>/surf/?h.w-g.pct.mgh || Gray to white matter signal intensity ratio, surface overlay ||
= Description =
[[pctsurfcon]] Calculates the gray to white matter signal intensity ratio (GWR).
= Examples =
== Example 1 ==
{{{
pctsurfcon --s bert
}}}

= Bugs =
None
= See Also =
[[wm-anat-snr]]
= Links =
None
= Methods Description =
{{{
description
description
}}}
= References =
[[References/Lastname###]]
= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
= Author/s =