Hi Doug, I tried to load the annotation and it gave an error. I look in the archives and I found someone with the same problem and the advice was to run:
recon-all -s <subject> -sd <subjects dir> -make all I did that and tried to run again mris_anatomical_stats as previously and still have this warning subj/stats/lh.aparc_lgi.stats subj lh computing statistics for each annotation in aparc.annot. using thickness file pial_lgi. reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white... reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial... reading input white surface /home/user/visao/Freesurfer//subj/surf/lh.white... MRISreadNewCurvature: incompatible vertex number in file /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi No such file or directory reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) structure is "bankssts" number of vertices = 1160 total surface area = 813 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.116 average integrated rectified Gaussian curvature = 0.031 folding index = 10 intrinsic curvature index = 1.3 structure is "caudalanteriorcingulate" number of vertices = 810 total surface area = 547 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.034 folding index = 9 intrinsic curvature index = 1.2 structure is "caudalmiddlefrontal" number of vertices = 4752 total surface area = 3134 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.123 average integrated rectified Gaussian curvature = 0.033 folding index = 48 intrinsic curvature index = 6.1 structure is "cuneus" number of vertices = 2701 total surface area = 1667 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.164 average integrated rectified Gaussian curvature = 0.061 folding index = 50 intrinsic curvature index = 7.1 (...) The LGI values are generated and they seem to be in the normal range as all the others... I would like to know if this problem invalidates all the other measures that I extracted (cortical thickness and surface area from aparc and Brodmann areas, aseg stats) Andreia Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > That probably means that the subject is out of synch. Try viewing the > subject's surface tksurfer or freeview and load the annotation. > doug > > On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote: >> >> Hello all, >> >> I generated the lgi.stats file for all my subjects and in one of them >> I got this warning: >> >> mris_anatomical_stats -a aparc.annot -t pial_lgi -f >> SUBJ/stats/lh.aparc_lgi.stats SUBJ lh >> computing statistics for each annotation in aparc.annot. >> using thickness file pial_lgi. >> reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz... >> reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white... >> reading input pial surface >> /home/user/visao/Freesurfer//SUBJ/surf/lh.pial... >> reading input white surface >> /home/user/visao/Freesurfer//SUBJ/surf/lh.white... >> *MRISreadAnnotationIntoArray: vertex index out of range: 150843 >> i=007D324B, in_array_size=150843 >> annot file: >> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot* >> MRISreadAnnotationIntoArray: vertex index out of range: 150844 >> i=007D324B, in_array_size=150843 >> annot file: >> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot >> MRISreadAnnotationIntoArray: vertex index out of range: 150845 >> i=007D324B, in_array_size=150843 >> annot file: >> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot >> >> (...) >> >> reading colortable from annotation file... >> colortable with 36 entries read (originally >> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >> structure is "bankssts" >> number of vertices = 1139 >> total surface area = 795 mm^2 >> total gray matter volume = 2868 mm^3 >> average cortical thickness = 3.820 mm +- 0.158 mm >> average integrated rectified mean curvature = 0.117 >> average integrated rectified Gaussian curvature = 0.031 >> folding index = 10 >> intrinsic curvature index = 1.3 >> structure is "caudalanteriorcingulate" >> number of vertices = 812 >> >> (...) >> >> Even thought there was the warning, everything seems to be fine with >> the lgi values, should I be concerned about this or I may just ignore it? >> >> Thank you! >> >> Andreia >> >> >> >> _______________________________________________ >> 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: 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 > > > 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 . 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