Hi Marie,
That was it, I forgot to run recon-all -localGI, thanks!
Everything worked fine for aparc, but for the Brodmann areas (BA) atlas I still get the warning, however the lgi values are generated (see attachments please).
Another question regards all other measures that I have obtained previously (before running -make all): I extracted thickness and pial surface area of Brodmann areas, Desikan-Killiany atlas and Destrieux atlas as well as aseg volumes. For BA I had to run mri_label2label and mris_label2annot to create a new BA.annot with the thresholded areas. To get the surface area values based on the pial surface I also had to run additional commands (mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.pial.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.a2009s.annot.ctab subj lh pial, for example)
I also ran qcache so to be able to do the vertex-wise analysis with qdec.
My question is: are all those measures/stats invalideted by this "MRISreadAnnotationIntoArray: vertex index out of range"? Should I run again any part of the proceesing for this subject?
Thank you so much!
Andreia
Quoting Marie Schaer <Marie.Schaer@unige.ch>:
> 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
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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/
>>>>
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