Sorry, it was the first command that failed. Run these two commands, then the mris_anatomical_stats mri_annotation2label --subject vol17 --hemi lh --lobesStrict lobesfile mri_annotation2label --subject vol17 --hemi rh --lobesStrict lobesfile
On 10/10/2012 12:24 PM, Carolina Valencia wrote: > 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 > <mailto: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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 * > > > _______________________________________________ > 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
