On 05/19/2014 04:10 PM, _andreia_@sapo.pt wrote:
I just ran vno_match_check for all my subjects and the scenario is:
*S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f subj1/stats/lh.BA_lgi.stats subj1 lh
the warning appears: *MRISreadAnnotationIntoArray*: vertex index out of range: 120389 i=0014C8B5, in_array_size=120388
*Only for Brodman* areas, not for Desikan-killiany nor Destrieux
vno_match_check: *no problem detected*!
vno_match_check was not checking the BA annot. I've fixed this and put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/vno_match_check
_*Subj2*_: mris_anatomical_stats -a BA.annot -t pial_lgi -f subj1/stats/lh.BA_lgi.stats subj1 lh
the warning appears for all parcellation (BA, aparc, aparc.a2009s), but *only for the lefh hemisphere*, everything's fine with the right.
vno_match_check: *erro for BOTH hemispheres*
Is it the the case that pial_lgi and BA.annot were created before the subject became out of synch? doug
These are conflicting information.
Any thoughts?
I cannot be sure of what to do...
Andreia
Quoting _andreia_@sapo.pt mailto:_andreia_@sapo.pt:
Hi Doug,
That's really bad news. So I'll check all my subjects to track the ones who give the error. Then I'll have to run each one from scratch?
I don't quite understand what went wrong with only a few subjects since I did (as far as I'm aware) everything in the same way for all of them. And what worries me the most now is that I only realized this because I wanted to extract the lgi values for the BA.thresh and the Destrieux atlas. If I stopped at just getting the thickness, the surface area and running qcahe as I have been doing for a while I wouldn't have noticed any problem.
So, the hard question again: will I need to run the ones that give this error from scratch or is there any other solution?
Thank you, Andreia
Quoting Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>:
On 05/19/2014 02:32 PM, _andreia_@sapo.pt
mailto:_andreia_@sapo.pt wrote:
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?
No, but you could write a little shell script to do it.
Does this invalidate all the measures I extracted and qcache?
Yes, I think so
Andreia
Quoting _andreia_@sapo.pt mailto:_andreia_@sapo.pt:
Hi Doug,
I just ran that command on the first subject I referred and the
output is:
[user@localhost mailto: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 <greve@nmr.mgh.harvard.edu
mailto:greve@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, _andreia_@sapo.pt
mailto:_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 mailto:_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
mailto: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
mailto:_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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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