Sorry for all the emails.. Now I ran that same command on the second subject in which I only detected a problem for the left hemisphere when trying to get Destrieux lgi, and got this error but for both hemispheres:
ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere has 121312 vertices Is there a way to check this in all subjects at once? Does this invalidate all the measures I extracted and qcache? Andreia Quoting _andre...@sapo.pt: > Hi Doug, > > I just ran that command on the first subject I referred and the output is: > >> [user@localhost Freesurfer]$ vno_match_check subj lh > Checking subj/surf/lh.orig... > Checking subj/surf/lh.white... > Checking subj/surf/lh.pial... > Checking subj/surf/lh.inflated... > Checking subj/surf/lh.smoothwm... > Checking subj/surf/lh.sphere... > Checking subj/surf/lh.curv... > Checking subj/surf/lh.sulc... > Checking subj/surf/lh.area... > Checking subj/surf/lh.thickness... > Checking subj/label/lh.aparc.annot... > Checking subj/label/lh.aparc.a2009s.annot... > Pass: all surfaces and surface data for subject subj have the same > number of vertices. > > Thank you! > > Andreia > > > Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
