Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ?
Kind Wishes, Anna On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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/ > >
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