BA.annot I think that was created before any problem because I had no error (at least I didn't see any) untill I extracted aparcstats2table of those values. But I just checked my notes and these two subjects were the only ones that gave aberrantly high LGI values when running -localGI. I then went to the mailing list and I saw posts with this error and it was suggested to run recon-all -autorecon2-wm -randomness which at that time solved the error and lgi computation went untill the end without any error.
I have no error notes for qcache that was ran previously.
Could I solve this issue running recon-all -autorecon2-cp/wm -autorecon3 (depending on the manual edits) and running again only the commands lgi and the ones to get pial surface area from Destrieux (since this was the only one I ran after the lgi error)? Or would it be safer to just run all commands to get BA thresholded, pial surface from Desikan-Killiany and Destrieux and all the necessary ones to get the stats?
Thank you very much for your help!
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
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 >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://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 >>>> mailto: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 >>> 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 > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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/