Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo
Can you check and see if they look ok with freeview? It might just be a display problem
On Apr 8, 2016, at 9:26 AM, pablo najt pablonajt@hotmail.com wrote:
Dear FS expert and users, We are coming across errors on the WM and Gray inflated surfaces. When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. <Screenshot.jpg> <Screenshot-1.jpg> Also when we try file-label-import annotation the following error occurs: colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt) Found embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate. Now we are trying to figure what is that could have caused this for all subjects. We have an old instructions for freesurfer saying to to run recon-all as follows. run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects. Any advise on this would be greatly appreciated. Cheers. Pablo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about loading annotation continues.In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes.Terminal shows endless column of the text below. Could there be that anything went wrong with the annotations? Any way to check for this and ideally correct without running entire recon-all again?Thanks a lotPablo
MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, in_array_size=181405 annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, in_array_size=181405 annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, in_array_size=181405 annot file: /Vo From: fischl@nmr.mgh.harvard.edu Date: Fri, 8 Apr 2016 09:56:46 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Can you check and see if they look ok with freeview? It might just be a display problem On Apr 8, 2016, at 9:26 AM, pablo najt pablonajt@hotmail.com wrote:
Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. <Screenshot.jpg> <Screenshot-1.jpg> Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
Hi Pablo
if it has the extension .label then it is a label not an annotation, and you should load it as such
cheers Bruce
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about loading annotation continues. In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes. Terminal shows endless column of the text below. Could there be that anything went wrong with the annotations? Any way to check for this and ideally correct without running entire recon-all again? Thanks a lot Pablo
MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, in_array_size=181405
annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, in_array_size=181405
annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, in_array_size=181405
annot file: /Vo
From: fischl@nmr.mgh.harvard.edu Date: Fri, 8 Apr 2016 09:56:46 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Can you check and see if they look ok with freeview? It might just be a display problem
On Apr 8, 2016, at 9:26 AM, pablo najt pablonajt@hotmail.com wrote:
Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces. When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. <Screenshot.jpg> <Screenshot-1.jpg> Also when we try file-label-import annotation the following error occurs: colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt) Found embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate. Now we are trying to figure what is that could have caused this for all subjects. We have an old instructions for freesurfer saying to to run recon-all as follows. run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects. Any advise on this would be greatly appreciated. Cheers. Pablo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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.
Thank you.I confirm, Annotation works fine. However when trying to load label and select .label file.I get the following message:
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)ERROR: LabelMarkSurface: label point 181451 exceeds nvertices 181405[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin12. named by Fri Apr 8 16:47:36 2016[0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Date: Fri, 8 Apr 2016 11:37:29 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Hi Pablo
if it has the extension .label then it is a label not an annotation, and you should load it as such
cheers Bruce
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about loading annotation continues. In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes. Terminal shows endless column of the text below. Could there be that anything went wrong with the annotations? Any way to check for this and ideally correct without running entire recon-all again? Thanks a lot Pablo
MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, in_array_size=181405
annot file:/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, in_array_size=181405
annot file:/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, in_array_size=181405
annot file: /Vo
From: fischl@nmr.mgh.harvard.edu Date: Fri, 8 Apr 2016 09:56:46 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Can you check and see if they look ok with freeview? It might just be a display problem
On Apr 8, 2016, at 9:26 AM, pablo najt pablonajt@hotmail.com wrote:
Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces. When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. <Screenshot.jpg>
<Screenshot-1.jpg>
Also when we try file-label-import annotation the following error occurs: colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt) Found embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate. Now we are trying to figure what is that could have caused this for all subjects. We have an old instructions for freesurfer saying to to run recon-all as follows. run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects. Any advise on this would be greatly appreciated. Cheers. Pablo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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
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.
label files don't store colortables, so it seems you are still loading annotations. Make sure you are using label loading. You can also specify them on the freeview command line with -l <label file name>
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you.I confirm, Annotation works fine. However when trying to load label and select .label file. I get the following message:
reading colortable from annotation file...
colortable with 76 entries read (originally/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_ surface_labels2009.txt)
colortable with 76 entries read (originally/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_ surface_labels2009.txt)
ERROR: LabelMarkSurface: label point 181451 exceeds nvertices 181405
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a darwin12. named by Fri Apr 8 16:47:36 2016
[0]PETSC ERROR: Libraries linked from/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2. 0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Date: Fri, 8 Apr 2016 11:37:29 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Hi Pablo
if it has the extension .label then it is a label not an annotation, and you should load it as such
cheers Bruce
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you Bruce for the response.Actually the surface works in freeview ju
st
fine. However my second issue about loading annotation continues. In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes. Terminal shows endless column of the text below. Could there be that anything went wrong with the annotations? Any way to check for this and ideally correct without running entire recon-all again? Thanks a lot Pablo
MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, in_array_size=181405
annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, in_array_size=181405
annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, in_array_size=181405
annot file: /Vo
__
From: fischl@nmr.mgh.harvard.edu Date: Fri, 8 Apr 2016 09:56:46 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Can you check and see if they look ok with freeview? It might just be a display problem
On Apr 8, 2016, at 9:26 AM, pablo najt pablonajt@hotmail.com wrote:
Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces. When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. <Screenshot.jpg> <Screenshot-1.jpg> Also when we try file-label-import annotation the following error occurs: colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt) Found embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate. Now we are trying to figure what is that could have caused this for all subjects. We have an old instructions for freesurfer saying to to run recon-all as follows. run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects. Any advise on this would be greatly appreciated. Cheers. Pablo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on
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 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
pablo najt