I think it is still out of synch. Try running vno_match_check subject lh
doug On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote: > Hello, > > Only after sending the email below I noticed that now the stats file > generated give only 0,00 were the LGI values should be, even though > they appear in the terminal. > > How can I solve this issue? And, again, are all the measures (cortical > thickness, surface area, aseg) invalidated? As well as qcache? In sum, > should I run this subject all from scratch? > > Thank you in advance, > Andreia Pereira > > > Quoting _andre...@sapo.pt: > >> 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 . 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. >> >> >> _______________________________________________ >> 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
