If the subject is out of synch, then running mris_preproc or recon-all -qcache should have failed too (as would have anything that tried to map the subject to a group space). This usually happens when you make edits to a subject but don't re-run the analysis all the way through (or the analysis fails). For the ones that are out of synch, you will need to re-run recon-all from the place where they went out of synch. Where that is exactly is hard to tell. Using recon-all -make all usually works but does not catch every possible case.
doug
On 05/19/2014 03:04 PM, _andreia_@sapo.pt wrote:
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 > 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/
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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/
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