Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise
it just prints to the screen.
mris_anatomical_stats
usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface
name>]
This program measures a variety of anatomical properties
valid options are:
-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 a file (different format than -b)
-log <log> - will write the stats into a file named <log>
-nsmooth <#> - will smooth the thicknessmap # of iterations before using
it
Jenni
On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ?
h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation.
I've tried using mris_anatomical_stats with various argument structures
(specifying output filenames, not specifiying output filenames) and can't
seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats
file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh
inflated -a mm103184/label/lh.aparc.splitcingulate.annot
reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/
wm.mgz...
reading input surface /Applications/freesurfer/subjects/reruns/
mm103184/surf/lh.inflated...
reading input surface /Applications/freesurfer/subjects/reruns/
mm103184/surf/lh.pial...
reading input surface /Applications/freesurfer/subjects/reruns/
mm103184/surf/lh.white...
done.
computing second fundamental form... ... done.
total white matter volume = 516178 mm^3
total surface area = 81462 mm^2
total gray matter volume = 230187 mm^3
average cortical thickness = 2.175 mm +- 0.836 mm
average integrated rectified mean curvature = 0.025
average integrated rectified Gaussian curvature = 0.096
folding index = 9766.477
intrinsic curvature index = 937.896
[catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
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