Hi,
Newbie question.
When I try to upload a surface to Freview I get the following error:
[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
Thanks, Kev
Can you send us the full command line and screen output? Cheers Bruce
On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,
Newbie question.
When I try to upload a surface to Freview I get the following error:
[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
Thanks, Kev _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Attached is the full command line; as per a screen output Freeview quits. I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks!
On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you send us the full command line and screen output? Cheers Bruce
On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,
Newbie question.
When I try to upload a surface to Freview I get the following error:
[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
Thanks, Kev
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.
I'll take a look, but in the future can you just send this as text embedded in the email instead of screen shots.
thanks Bruce
On Sat, 27 May 2017, Schumman Resonance wrote:
Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks!
On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Can you send us the full command line and screen output? Cheers Bruce
On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,Newbie question.
When I try to upload a surface to Freview I get the following error:
[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
Thanks, Kev
_______________________________________________ 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.
actually the attachment doesn't have an extension, so I can't even look at it. Can you just resend as text?
cheers Bruce On Sat, 27 May 2017, Schumman Resonance wrote:
Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks!
On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Can you send us the full command line and screen output? Cheers Bruce
On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,Newbie question.
When I try to upload a surface to Freview I get the following error:
[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
Thanks, Kev
_______________________________________________ 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.
The error message says it:
ERROR: MRISread: file '/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
You were not loading a correct surface file. lh.area.pial is a scalar data file. Maybe you wanted to load lh.pial?
Ruopeng
On May 28, 2017, at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
actually the attachment doesn't have an extension, so I can't even look at it. Can you just resend as text?
cheers Bruce On Sat, 27 May 2017, Schumman Resonance wrote:
Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks! On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Can you send us the full command line and screen output? Cheers Bruce On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,Newbie question. When I try to upload a surface to Freview I get the following error:
[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 Thanks, Kev
_______________________________________________ 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
Thanks that makes sense! here is the text file and embedded just in case there is anything else to it Thanks!
"Last login: Sat May 27 20:26:15 on ttys000 -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni
schummans-MacBook-Pro:~ schumman$ freeview 2017-05-27 21:06:49.672 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.672 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.684 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.684 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.695 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.695 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.706 Freeview[36047:303] invalid drawable 2017-05-27 21:06:49.706 Freeview[36047:303] invalid drawable 2017-05-27 21:07:07.035 Freeview[36047:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: 2017-05-27 21:10:03.377 Freeview[36047:303] -_continuousScroll is deprecated for NSScrollWheel. Please use -hasPreciseScrollingDeltas. 2017-05-27 21:10:03.377 Freeview[36047:303] -deviceDeltaX is deprecated for NSScrollWheel. Please use -scrollingDeltaX. 2017-05-27 21:10:03.377 Freeview[36047:303] -deviceDeltaY is deprecated for NSScrollWheel. Please use -scrollingDeltaY. nquads=6225924, nvertices=560 ERROR: MRISread: file '/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
robably trying to use a scalar data file as a surface! 0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial' has many more faces than vertices! [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 schummans-MacBook-Pro.local by schumman Sat May 27 21:06:49 2017 [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 schummans-MacBook-Pro:~ schumman$ “
On May 28, 2017, at 8:10 AM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
The error message says it:
ERROR: MRISread: file '/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
You were not loading a correct surface file. lh.area.pial is a scalar data file. Maybe you wanted to load lh.pial?
Ruopeng
On May 28, 2017, at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
actually the attachment doesn't have an extension, so I can't even look at it. Can you just resend as text?
cheers Bruce On Sat, 27 May 2017, Schumman Resonance wrote:
Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks! On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Can you send us the full command line and screen output? Cheers Bruce On May 27, 2017, at 11:45 PM, Schumman Resonance schummanr@gmail.com wrote:
Hi,Newbie question. When I try to upload a surface to Freview I get the following error:
[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 Thanks, Kev
_______________________________________________ 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Freesurfer -
Ruopeng Wang -
Schumman Resonance