Hi Andreia,
You probably have lGI values that correspond to earlier versions of your surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces and reprocessed them, but forgot to recalculate lGI for this new surfaces).
If you simply reprocess lGI now, that should solve the problem.
If not let me know,
Marie
On May 16, 2014, at 1:08 PM, "_andreia_@sapo.pt" _andreia_@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 _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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