I just ran vno_match_check for all my subjects and the scenario is:
Subj1: 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!
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
These are conflicting information.
Any thoughts?
I cannot be sure of what to do...
Andreia
Quoting _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>:
>
>> On 05/19/2014 02:32 PM, _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:
>>>
>>>> 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 <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 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>> greve@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
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>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>> --
>>>>> Douglas N. Greve, Ph.D.
>>>>> MGH-NMR Center
>>>>> greve@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
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>>>
>>> _______________________________________________
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>>> 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
>> 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