Differences between revisions 1 and 10 (spanning 9 versions)

Index

Contents

Name
Synopsis
Arguments
Outputs
Description
Examples
1. Example 1
2. Example 2
Bugs
See Also
Links
Methods Description
References
Reporting Bugs
Author/s

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

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

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

Bugs

none

Links

FreeSurfer

Methods Description

??

References

References/Lastname###

Reporting Bugs

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

Author/s

BruceFischl

-  ⇤ ← Revision 1 as of 2004-09-10 11:50:05 → 
  Size: 1656
  Editor: DavidTuch
  Comment: new page
+   ← Revision 10 as of 2009-01-05 18:24:46 → ⇥
  Size: 2665
  Editor: KrishSubramaniam
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 10:
-[[TableOfContents]]
+<<TableOfContents>>
 Line 36:
+||-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||
-Line 39:
+Line 44:
-|| ?? || ?? ||
+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 ||
-Line 42:
+Line 58:
-["mris_anatomical_stats"] computes a number of anatomical properties
+[[mris_anatomical_stats]] computes a number of anatomical properties
-Line 46:
+Line 62:
-??
+{{{
mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh
}}}
-Line 55:
+Line 72:
-["othercommand1"], ["othercommand2"]
+[[mris_curvature_stats]],
-Line 66:
+Line 83:
-["References/Lastname###"]
+[[References/Lastname###]]