I think it would be --parc aparc.pial_lgi
doug On 11/14/2013 11:27 AM, Anna Jonsson wrote: > Thank you. Can I then use > aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc > lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in > 1 tablefile or should I use other command? > > > On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > yes and yes > > > On 11/13/2013 12:04 PM, Anna Jonsson wrote: > > Thank you very much. By second I assume you mean second row? > And out of the values on the second row it must be the value > 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? > > Thanks again > > > > On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > that looks correct. It is the 2nd number you want. The > first is > for the > medial wall (not interesting). You can have it report only for > cortex by > adding --id 1 > > doug > > > On 11/13/2013 11:45 AM, Anna Jonsson wrote: > > Dear list, > > > > I have a question about extracting global lgi > values/hemisphere. I > > think I have managed to do it correctly using : > > > > mri_segstats --slabel subj lh > $SUBJECTS_DIR/subj/label/lh.cortex --i > $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum > lh.aparc.pial_lgi.stats > > > > (Please let me know if this is not correct) > > > > > > I then get this output ( for each individual) > > > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean > StdDev Min Max Range > > 1 0 7953 5220.0 Seg0000 2.4055 0.4052 > <tel:2.4055%20%20%200.4052> 1.5796 2.9763 1.3967 > > > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 > 1.7030 6.0007 4.2977 > > > > I assume one of these values (if above command has worked > correctly) contains the mean lgi value for the left > hemisphere. > Can somebody please tell me which of the above values is the > correct lgi value? Additionally, what units are lgi > measured in, > and are values between 1-5 what is considered normal? > > > > > > Thank you very much > > > > Anna > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
