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,
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.
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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 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,
--
*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 greve@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
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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.
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 <greve@nmr.mgh.harvard.edu mailto: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, > > -- > -- > *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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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Carolina Valencia -
Douglas N Greve