[Freesurfer] PETSC ERROR
Hi I posted a couple days ago about a PETSC ERROR with while running mri_cvs_register but I seem to be having a more general problem. I'm receiving the same error on two 10.6.7 macs as well as on a Windows running virtualbox, both while processing my own subjects and FS5.1 bert. I'm using the command mri_cvs_register --mov bert --template cvs_avg35 and between step = 17 and step = 12 (break point is consistent within the individual but differs between individuals) I receive the same PETSC error (end of log appended below). In the VB I doubled the amount of memory allocated to the system and bert crashed as the same point in the process. Thanks in advance David step = 16 === elt_vol= 19.8125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 6.32 Smoothing mesh. Smooth seconds: 0.41 Writing nodes. Writing elements. Writing faces. Output seconds: 0.03 Total running seconds: 6.76 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 62502 Mesh tetrahedra: 372867 Mesh faces: 755978 Mesh subfaces: 20488 Mesh subsegments: 465 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 62502 mesh elts = 372867 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 10 elapsed = 0.307 seconds element count = 1457735 count inserted = 20 elapsed = 0.44 seconds element count = 3996981 count inserted = 30 elapsed = 0.338 seconds element count = 6263194 done building octree - total elements = 7845082 penalty_weight = 1000 setting bc 205.891 174.948 225.515 - 0 0 0 instead 205.881 174.938 225.505 - norm = 0.0173205 setting bc 205.891 174.948 27.6148 - 0 0 0 instead 205.881 174.938 27.6248 - norm = 0.0173205 setting bc 205.891 35.1985 225.515 - 0 0 0 instead 205.881 35.2085 225.505 - norm = 0.0173205 setting bc 205.891 35.1985 27.6148 - 0 0 0 instead 205.881 35.2085 27.6248 - norm = 0.0173205 setting bc 52.3002 174.948 225.515 - 0 0 0 instead 52.3102 174.938 225.505 - norm = 0.0173205 setting bc 52.3002 174.948 27.6148 - 0 0 0 instead 52.3102 174.938 27.6248 - norm = 0.0173205 setting bc 52.3002 35.1985 225.515 - 0 0 0 instead 52.3102 35.2085 225.505 - norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 - 0 0 0 instead 52.3102 35.2085 27.6248 - norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 83286 Total BCs = 548640 no-eqs = 187506 [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 1973583872 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 225757228! [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: surf2vol on a linux-gnu named FreeSurfer by virtualuser Tue Jun 21 12:18:59 2011 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --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: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out
[Freesurfer] error during mri_cvs_register
Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David -LOG-- step = 12 === elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788 Writing nodes. Writing elements. Writing faces. Output seconds: 0.036639 Total running seconds: 4.61682 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 10 elapsed = 0.302 seconds element count = 1128168 count inserted = 20 elapsed = 0.496 seconds element count = 3256402 count inserted = 30 elapsed = 0.411 seconds element count = 5222879 count inserted = 40 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 - 0 0 0 instead 205.881 174.938 225.505 - norm = 0.0173205 setting bc 205.891 174.948 27.6148 - 0 0 0 instead 205.881 174.938 27.6248 - norm = 0.0173205 setting bc 205.891 35.1985 225.515 - 0 0 0 instead 205.881 35.2085 225.505 - norm = 0.0173205 setting bc 205.891 35.1985 27.6148 - 0 0 0 instead 205.881 35.2085 27.6248 - norm = 0.0173205 setting bc 52.3002 174.948 225.515 - 0 0 0 instead 52.3102 174.938 225.505 - norm = 0.0173205 setting bc 52.3002 174.948 27.6148 - 0 0 0 instead 52.3102 174.938 27.6248 - norm = 0.0173205 setting bc 52.3002 35.1985 225.515 - 0 0 0 instead 52.3102 35.2085 225.505 - norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 - 0 0 0 instead 52.3102 35.2085 27.6248 - norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 29571! [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: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see
Re: [Freesurfer] error during mri_cvs_register
Thanks for the advice Priti, I deleted the old cvs files and re-ran but still no luck. I also tried a new subject on a different Mac (still 10.6.7) and received the same error. Thanks David On Mon, Jun 20, 2011 at 12:56 PM, rspr...@nmr.mgh.harvard.edu wrote: Hi David, I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you. Thanks, Priti Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David -LOG-- step = 12 === elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788 Writing nodes. Writing elements. Writing faces. Output seconds: 0.036639 Total running seconds: 4.61682 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 10 elapsed = 0.302 seconds element count = 1128168 count inserted = 20 elapsed = 0.496 seconds element count = 3256402 count inserted = 30 elapsed = 0.411 seconds element count = 5222879 count inserted = 40 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 - 0 0 0 instead 205.881 174.938 225.505 - norm = 0.0173205 setting bc 205.891 174.948 27.6148 - 0 0 0 instead 205.881 174.938 27.6248 - norm = 0.0173205 setting bc 205.891 35.1985 225.515 - 0 0 0 instead 205.881 35.2085 225.505 - norm = 0.0173205 setting bc 205.891 35.1985 27.6148 - 0 0 0 instead 205.881 35.2085 27.6248 - norm = 0.0173205 setting bc 52.3002 174.948 225.515 - 0 0 0 instead 52.3102 174.938 225.505 - norm = 0.0173205 setting bc 52.3002 174.948 27.6148 - 0 0 0 instead 52.3102 174.938 27.6248 - norm = 0.0173205 setting bc 52.3002 35.1985 225.515 - 0 0 0 instead 52.3102 35.2085 225.505 - norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 - 0 0 0 instead 52.3102 35.2085 27.6248 - norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 29571! [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: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options
[Freesurfer] Averaging Labels
Hi, I’m trying to average 2 labels together, but haven’t seen any script out there that does this. Essentially we used ROI localizer tasks to create individual labels for each of our subjects. For visualization purposes, we created an average brain, and used mri_label2label to map each individual subjects’ label onto the group brain. But, now I’m not sure how to create an average of these labels. Thanks! David Brang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
