Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
Hi Knut Jørgen - Do you get this error only with the dev version of freesurfer? The command line causing the error is: bbregister --s 4_test --init-fsl --dti --mov /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat /home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat Can you please try running this with the 5.3 version? Thanks! a.y On Wed, 13 Jul 2016, Knut J Bjuland wrote: Hi Anastasia Thanks. I am sending my entire trac-all.log Knut Jøgen On 07/12/2016 11:19 PM, Anastasia Yendiki wrote: Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/ref vol.fslregister.nii -in /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/mov vol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fs l.mat -init /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fsl mat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Fedora 24 glibc-2.23.1-8.fc24.x86_64 gcc-6.1.1-3.fc24.x86_64 libstdc++-6.1.1-3.fc24.x86_64 ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x7feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000) Knut Jørgen Bjuland ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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.
Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
Hi Anastasia Thanks. I am sending my entire trac-all.log Knut Jøgen On 07/12/2016 11:19 PM, Anastasia Yendiki wrote: Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii -in /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat -init /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Fedora 24 glibc-2.23.1-8.fc24.x86_64 gcc-6.1.1-3.fc24.x86_64 libstdc++-6.1.1-3.fc24.x86_64 ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x7feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000) Knut Jørgen Bjuland ___ 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. Wed Jul 13 16:32:42 CEST 2016 /home/knutjbj/subjects /usr/local/freesurfer/bin/trac-all -prep -c dmric.4_test Subject 4_test SUBJECTS_DIR /home/knutjbj/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer60 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160706-3f44648 knutjbj loalhost Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 127405 maxlocks unlimited maxsignal127405 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 32845380 962006816527136 169380 669817622482108 Swap: 71678968 071678968 Program versions: $Id: trac-all,v 1.60 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $
Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii -in /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat -init /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Fedora 24 glibc-2.23.1-8.fc24.x86_64 gcc-6.1.1-3.fc24.x86_64 libstdc++-6.1.1-3.fc24.x86_64 ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x7feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000) Knut Jørgen Bjuland ___ 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] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
flirt.fsl -ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 -verbose 0 -omat/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat-init/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.schterminate called after throwing an instance of'NEWMAT::SingularException'Abort (core dumped) ERROR: flirtFedora 24glibc-2.23.1-8.fc24.x86_64gcc-6.1.1-3.fc24.x86_64libstdc++-6.1.1-3.fc24.x86_64ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)libstdc++.so.6 => /lib64/libstdc++.so.6(0x7feaeb67e000)libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000)libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000)libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)Knut Jørgen Bjuland ___ 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.
