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

---

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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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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.

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 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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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.

---

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---

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Hello again,

Sorry for not waiting for your reply, but I realized that I get the same warning with another different subject when trying to get destrieux lgi and this happens only for the left hemisphere:

[user@localhost Freesurfer]# mris_anatomical_stats -a aparc.a2009s.annot -t pial_lgi -f subj/stats/lh.aparc.a2009s_lgi.stats subjs lh

computing statistics for each annotation in aparc.a2009s.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: 120388 i=0014C8B5, in_array_size=120388 annot file: /home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot MRISreadAnnotationIntoArray: vertex index out of range: 120389 i=0014C8B5, in_array_size=120388 annot file: /home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot MRISreadAnnotationIntoArray: vertex index out of range: 120390 i=0014C8B5, in_array_size=120388 annot file: /home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot

(...)

With the first subject this happens only for Brodman areas, in both hemispheres.

The thing is that the lgi values look alright when I look at them among all the other subjects...

Any thoughts?

Thank you very much!

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 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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---

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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

---

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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/

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---

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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!

_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.ptwrote:

...

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@localhostFreesurfer]$ 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.ptwrote:

...

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.ptwrote: >>> 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[1] >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html[2] >> 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[1] FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html[2] 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[1] FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html[2] Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Ligações: --------- [1] <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a> [2] <a href="http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html"> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html</a>

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/

Hi Marie,

Thanks for the input! Actually, from the recon-all log I can see that autorecon3 was caled in the terminal, and comparing it to a subject without any error they look the same to me. Also, qcache gave no error.

Anyway, I'll rerun -autorecon3 for these 2 subjects and all the commands to get the specific stats (BA.thresholed, pial area from the 3 parcellations, aparc, aparc.a2009s and BA) as well as qcache.

Andreia

Quoting Marie Schaer Marie.Schaer@unige.ch:

Hi Andreia,

Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. As the randomness flag changes the number of vertices when recreating the surfaces, that explains the error. So for your subjects, just rerun autorecon3 (and qcache and mris_anatomical_stats), and you should be fine. But if I were you I would then carefully check for all my subjects that registration (i.e. autorecon3) was processed after autorecon2, and then qcache / mris_anatomical_stats after autorecon3 (my understanding is that without the randomness flag that kind of errors can be more difficult to trace back as the number of vertices remain the same).

Best,

Marie

On May 19, 2014, at 3:55 PM, _andreia_@sapo.pt wrote:

...

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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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 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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Hi Andreia

I haven't been following this whole thread, but the matlab warning is not a problem

cheers Bruce On Tue, 20 May 2014, _andreia_@sapo.pt wrote:

Hi,

Do I need to run laleb2label and label2annot to get once again the BA.thresh?

Or is it enough to just extract the stats?

I already extracted the aseg stats and one of the subjects came out with slightly different values this time, while the other presented the same values. Was this supposed to happen?

Another question: when I run recon-all -s subj -localGI I get a warning from matlab:

Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.

                        < M A T L A B (R) >
              Copyright 1984-2013 The MathWorks, Inc.
                R2013a (8.1.0.604) 64-bit (glnxa64)
                         February 15, 2013

To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.

Is this problematic?

Thanks for the patient! Andreia

Quoting Marie Schaer Marie.Schaer@unige.ch:

...

Hi Andreia,

Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. As the randomness flag changes the number of vertices when recreating the surfaces, that explains the error. So for your subjects, just rerun autorecon3 (and qcache and mris_anatomical_stats), and you should be fine. But if I were you I would then carefully check for all my subjects that registration (i.e. autorecon3) was processed after autorecon2, and then qcache / mris_anatomical_stats after autorecon3 (my understanding is that without the randomness flag that kind of errors can be more difficult to trace back as the number of vertices remain the same).

Best,

Marie

On May 19, 2014, at 3:55 PM, _andreia_@sapo.pt wrote:

...

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/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> 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

-- 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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If you ran with -autorecon3, then you do not need to redo the labels. As for the aseg, it depends on what you ran and what edits you made. If you ran with -autorecon2 and you had added control points, then it would change slightly.

You can ignore that matlab warning (it is only saying that you cannot create figures and such, which you would not want to do under the circumstances)

doug

On 05/20/2014 05:19 AM, _andreia_@sapo.pt wrote:

Hi,

Do I need to run laleb2label and label2annot to get once again the BA.thresh?

Or is it enough to just extract the stats?

I already extracted the aseg stats and one of the subjects came out with slightly different values this time, while the other presented the same values. Was this supposed to happen?

Another question: when I run recon-all -s subj -localGI I get a warning from matlab:

Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.

                          < M A T L A B (R) >
                Copyright 1984-2013 The MathWorks, Inc.
                  R2013a (8.1.0.604) 64-bit (glnxa64)
                           February 15, 2013

To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.

Is this problematic?

Thanks for the patient! Andreia

Quoting Marie Schaer Marie.Schaer@unige.ch:

...

Hi Andreia,

Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. As the randomness flag changes the number of vertices when recreating the surfaces, that explains the error. So for your subjects, just rerun autorecon3 (and qcache and mris_anatomical_stats), and you should be fine. But if I were you I would then carefully check for all my subjects that registration (i.e. autorecon3) was processed after autorecon2, and then qcache / mris_anatomical_stats after autorecon3 (my understanding is that without the randomness flag that kind of errors can be more difficult to trace back as the number of vertices remain the same).

Best,

Marie

On May 19, 2014, at 3:55 PM, _andreia_@sapo.pt wrote:

...

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/ >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> 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

-- 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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