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 _andreia_@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 greve@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, _andreia_@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
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