Dear FreeSurfer experts,
I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL.
For example, given two images, I want to know the brain regions in image1 but not in image2.
Could you please recommend the general command line tools I can use for these purposes?
Many thanks, Daniel
Hi Daniel
you can always convert to nifti via:
mri_convert cluster.mgh cluster.nii
and you will be able to use the FSL tools
cheers Bruce
On Tue, 3 Nov 2015, Yang, Daniel wrote:
Dear FreeSurfer experts,
I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL.
For example, given two images, I want to know the brain regions in image1 but not in image2.
Could you please recommend the general command line tools I can use for these purposes?
Many thanks, Daniel
Hi Bruce,
Yes, that’s perfect! Thanks for the reply!! :)
Best, Daniel
On 11/2/15, 8:48 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel
you can always convert to nifti via:
mri_convert cluster.mgh cluster.nii
and you will be able to use the FSL tools
cheers Bruce
On Tue, 3 Nov 2015, Yang, Daniel wrote:
Dear FreeSurfer experts,
I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL.
For example, given two images, I want to know the brain regions in image1 but not in image2.
Could you please recommend the general command line tools I can use for these purposes?
Many thanks, Daniel
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHY&m=xYv-TPUIzaxdOU0_l0VVahSrl6jSBd6Rbsb4dfB0Jak&s=uRT7WmDS-H I2mX7rEaBPdsfzQTjJgPVdORtlxQzhgvw&e= . 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.
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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 Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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.
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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
Our IT guy said it could be a software problem since he didn't have the problem and the only difference between out computers was the display. We have these versions at the institute:
4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta Is the first one the dev version?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 17:57:50 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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... [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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
_______________________________________________ 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
_______________________________________________ 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.
Try 6.0.0beta.
On 11/03/2015 12:02 PM, Clara Kühn wrote:
Our IT guy said it could be a software problem since he didn't have the problem and the only difference between out computers was the display. We have these versions at the institute:
4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta Is the first one the dev version?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 17:57:50 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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... [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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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
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
With the FS 6 beta version the problem doesn't occur. Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 18:03:52 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Try 6.0.0beta.
On 11/03/2015 12:02 PM, Clara Kühn wrote:
Our IT guy said it could be a software problem since he didn't have the problem and the only difference between out computers was the display. We have these versions at the institute:
4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta Is the first one the dev version?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 17:57:50 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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... [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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Ruopeng,
I tried different computers and on most of them it works when I test-delete a wm voxel and then save the wm.mgz. However, when I then go on to actually editing the wm.mgz Freeview crashes when I hit "save" as it's done on my computer. I've tried not using the button but going through the menu "save volume" and I tried "save as" under a different name. Still crashes. I've done all my editing with FS 5.3.0 and I don't think it's a good idea to switch versions mid-editing.
Do you have an idea whether there might be a setting or a feature or whatever that I can change and what this part of the error message means: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "ckuehn" ckuehn@cbs.mpg.de An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 4. November 2015 08:07:44 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
With the FS 6 beta version the problem doesn't occur. Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 18:03:52 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Try 6.0.0beta.
On 11/03/2015 12:02 PM, Clara Kühn wrote:
Our IT guy said it could be a software problem since he didn't have the problem and the only difference between out computers was the display. We have these versions at the institute:
4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta Is the first one the dev version?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 17:57:50 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Hi Bruce,
I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 3. November 2015 14:42:25 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it crash?
thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.
I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version. Here is the error message I get in the terminal:
[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... [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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn
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
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
_______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Clara Kühn -
Ruopeng Wang -
Yang, Daniel