Hi Alex,
did you run mris_ca_train with -t <color table>? If so, it should embed
the color table in the .gcs file, then get probagated to the .annot, so
you shouldn't have to specify anything to mris_anatomical_stats.
cheers,
Bruce
On Fri, 30
Dec 2005, Fornito, Alexander wrote:
Hi,
I'm trying to run mris_anatomical_stats on a custom parcellation, but am having
problems because I don't know what the flag to speficy the appropriate colour
table is. If I run the -b option, I get output but with no labels. If I run -f,
I get a message saying that no colour table is loaded. Commands and output are
below.
Thanks,
Alex
mris_anatomical_stats -mgz -a acc.annot -b 1000908 lh white
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in acc.annot.
reading volume
/data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz...
reading input surface
/data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white...
INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found.
done.
computing second fundamental form... ... done.
total white matter volume = 442238 mm^3
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
111575 75355 185201 2.472 +- 0.836 0.190 0.061 1980.885 250.831
** annotation 003c1400
444 269 715 2.685 +- 0.637 0.110 0.021 1.601 0.402 **
annotation 00dc3c3c
891 578 1588 2.777 +- 0.537 0.187 0.034 15.162 1.149 **
annotation 003c3c8c
213 126 392 3.145 +- 0.924 0.152 0.034 2.943 0.297 **
annotation 003c6464
82 40 152 3.785 +- 0.634 0.070 0.011 0.196 0.034 **
annotation 00b4648c
567 334 906 2.723 +- 0.503 0.103 0.020 2.385 0.434 **
annotation 00b48c3c
1093 709 2195 3.051 +- 0.793 0.206 0.078 20.688 3.225 **
annotation 003c643c
240 139 311 2.247 +- 0.872 0.085 0.010 0.454 0.149 **
annotation 008c143c
*OR*
mris_anatomical_stats -mgz -a acc.annot -f ./1000908.txt 1000908 lh white
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in acc.annot.
reading volume
/data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz...
reading input surface
/data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white...
INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found.
done.
computing second fundamental form... ... done.
total white matter volume = 442238 mm^3
mris_anatomical_stats: no color table loaded - cannot translate annot file
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
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