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


= Name =
mris_anatomical_stats - measures a number of anatomical properties

= Synopsis =
mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>]

= Arguments =
== Required Positional Arguments ==
|| <subjectname>|| subject name ||
|| <hemi> || hemisphere ||

== Optional Positional Arguments ==
|| <surfacename> || surface name ||

== Required Flagged Arguments ==
none

== Optional Flagged Arguments ==
||-i  <low thresh> <hi thresh> || only consider thicknesses in the specified range. ||
||-l <label file> || limit calculations to specified label||
||-t <thickness file> || use specified file for computing thickness statistics ||
||-a <annotation file> || compute properties for each label in the annotation file separately ||
||-b || tabular output ||
||-f <tablefile> ||table output to tablefile (different format than -b). Must use -a or -l options to spec input.||
||-log <logfile> || Write stats to file named log ||
||-nsmooth <#> || Smooth thicknessmap # of iterations before using it ||
||-c <ctab file> || Output annotation files's colortable to text file||
||-noglobal || Do not compute global brain stats ||
||-th3 || Compute vertex-wise volume by dividing each obliquely truncated trilateral pyramid into three tetrahedra ||


= Outputs =
Tabular output includes the following:
|| '''Data column''' || '''units''' || '''Comments''' ||
||Structure Name || NA || ||
||Number of Vertices || unitless ||
||Surface Area || mm^2 || total surface area ||
||Gray Matter || Volume mm || total gray matter volume ||
||Average Thickness || mm || average cortical thickness  ||
||Thickness Std Dev || mm ||+- standard error (mm) ||
||Integrated Rectified Mean Curvature || mm^-1 || ||
||Integrated Rectified Gaussian Curvature || mm^-2 || ||
||Folding Index || unitless || a la Van Essen ||
||Intrinsic Curvature Index || unitless || a la Van Essen ||

= Description =
mris_anatomical_stats computes a number of anatomical properties

= Examples =
== Example 1 ==
{{{
mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh
}}}
== Example 2 ==
{{{
mris_anatomical_stats -l lh.cortex.label -b subjid lh
}}}

= Bugs =
none

= See Also =
[[mris_curvature_stats]], 

= Links =
FreeSurfer

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

= Author/s =
BruceFischl