I've tried your suggestion, but I don't succeed, first I look for all the option of the command mris_anatomical_stats and I don't understand some of them, like the last word white and the -cortex option.
If I finally succeed, where I can find the values? Can I visualize a colored brain based on the lobes?
Many thanks.
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/CORBIC_vol17/CORBIC_vol17/scripts> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile -b -a ../label/lh.lobesfiles.annot CORBIC_vol17 lh white
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
computing statistics for each annotation in ../label/lh.lobesfiles.annot.
reading volume /home/cvalencia/freesurfer/subjects/volumetria/CORBIC_vol17/CORBIC_vol17/mri/wm.mgz...
reading input surface /home/cvalencia/freesurfer/subjects/volumetria/CORBIC_vol17/CORBIC_vol17/surf/lh.white...
reading input pial surface /home/cvalencia/freesurfer/subjects/volumetria/CORBIC_vol17/CORBIC_vol17/surf/lh.pial...
reading input white surface /home/cvalencia/freesurfer/subjects/volumetria/CORBIC_vol17/CORBIC_vol17/surf/lh.white...
could not read annot file ../label/lh.lobesfiles.annot
No such file or directory
mris_anatomical_stats: could not read annotation file ../label/lh.lobesfiles.annot
No such file or directory
2012/10/9 Douglas N Greve
<greve@nmr.mgh.harvard.edu>
Try this
cd $SUBJECTS_DIR/subject/scripts
mri_annotation2label --subject vol17 --hemi rh --lobesStrict lh.lobesfile
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject
lh white
doug
On 10/05/2012 09:53 AM, Carolina Valencia wrote:
> Hi FS users and developers,
>
> I need to obtain the volume per lobe (occipital, parietal, temporal,
> frontal) in a particular subjects and if it is possible divided by
> gray and white matter.
> I found similar topics in the mailing list, but I don't succeed to get
> this values.
> I follow the instructions for the FSv5.1 Using mri_annotation2label
> and mris_anatomical_stats but I got values for each hemisphere
> instead of lobes.
> mri_annotation2label --subject vol17 --hemi rh --lobesStrict rhlobesfile
> mri_annotation2label --subject vol17 --hemi lh --lobesStrict lhlobesfile
> then:
> mris_anatomical_stats vol17 rh
> mris_anatomical_stats vol17 lh
> I got values
> number of vertices = 115348
> total surface area = 76188 mm^2
> total gray matter volume = 282811 mm^3
> average cortical thickness = 3.071 mm +- 1.034 mm
> average integrated rectified mean curvature = 0.149
> average integrated rectified Gaussian curvature = 0.106
> folding index = 4797
> intrinsic curvature index = 391.1
>
> Can somebody guide me?
>
> Thank you in advance,
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
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Carolina Valencia