Hi Douglas, 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 <gr...@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, > > > > -- > > -- > > *Carolina Valencia > > * > > > > The information contained in this message and its attachments is > > confidential and intended for exclusive use of the recipients. If you > > received this email by error please notify the sender and delete it. > > The use, retention or distribution for any purpose is prohibited. Link > > is not responsible for damage caused by the contents of this message. > > The recipient should check for any presence of viruses or other defects. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- -- *Carolina Valencia *
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