[Freesurfer] Freeview Crashes!!
Dear FS Experts, While using updated Freeview in ubuntu 16.04, I reproducibly get two following errors: 1st Crash (While selecting color for the volume): Volume - Colormap -Lookup Table option: 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv 2nd Error/Crash: Loaded lh.pial and rh.pial surfaces + a volume activated as an isosurface. Now while rotating the 3D window Freeview crashes with following error: Did not find any volume info p9\d�Did not find any volume info p9\d�[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/p etsc-as/documentation/troubleshooting.html#Signal[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 WS52 by wiki Thu Nov 9 16:29:50 2017 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/L inux2-2.3-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 # I don't think RAM/memory is an issue, as the computer has 65GB RAM. Any other options/update I should try? I am planning to load multiple volumes as isosurface in multiple colors, and show them with lh.pial and rh.pial. Thank you very much ___ 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] fs on GPU? Segmentation fault error!
External Email - Use Caution Freesurfer Wizards, Any thoughts on this? Thanks in advance ## *I renamed:* /usr/local/cuda-8.0/lib64$ sudo cp libcudart.so.8.0 libcudart.so.5.0 *in the next step:* recon-all -i $sub_dir/$i/"$i".nii -all -sd $output_dir $i -use-gpu . . Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 9.20 Runtime : 8.0 Acquiring CUDA device Using default device CUDA device: TITAN Xp *Segmentation fault * Linux Dond-12 1.25.0-13-generic #36~16.04.1-Ubuntu SMP Wed Aug 15 17:21:05 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2 exited with ERRORS at Mi 6. Feb 18:14:50 CET 2019 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mni152reg ends with (ERROR: flirt)
External Email - Use Caution Dear Freesurfer Experts! The idea is to transform freesurfer output in to the MNI 1mm space using following command: mni152reg --s subject_id --1 But mni152reg crashes with following error: flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' ERROR: flirt Your help is appreciated! Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error running recon-all
External Email - Use Caution Dear Freesurfer experts, Greetings! In the first minute of recon-all, we are getting following error: mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at slice 0 T1 data type is int16, data type 4 (looked using fslinfo) Looking forward to have your input! Thank you so much, Kind regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error running recon-all
External Email - Use Caution Please also find recon-all.log file. Thanks! On Thu, Jul 25, 2019 at 6:50 AM vin rasa wrote: > Dear Freesurfer experts, > Greetings! > > > In the first minute of recon-all, we are getting following error: > > mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at > slice 0 > > > T1 data type is int16, data type 4 (looked using fslinfo) > > Looking forward to have your input! > > Thank you so much, > Kind regards > > Mi 24. Jul 17:45:53 CEST 2019 /media/results/test /usr/local/freesurfer/bin/recon-all -i /home/Downloads/reorient/test.nii -all -sd /media/results/Oasis -s test subjid test setenv SUBJECTS_DIR /media/results/Oasis FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux tuffan 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 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 257062 maxlocks unlimited maxsignal257062 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 6587885662267900 613692 1379984 2997264 1411128 Swap: 62606332 727946855326864 program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/07/24-15:45:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: vin Machine: tuffan Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ Time
[Freesurfer] Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects
External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4 structures only. I found aparcstats2table command, which seems to extract all the segmented regions. https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table Thanks in advance ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all ends in 4 seconds without error!!
External Email - Use Caution Dear Freesurfer Experts, Greetings! I am trying to run freesurfer on Synthetic T1 data (see in snapshot: *''Simulated T1 image', last sentence in the snapshot*') from Brainweb ( https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6dr5d7BqISQ4OX0IXN53ZgfgLg7fOkHGB7XNRBVvnJnU9CE4TEtRcWizxFRY_pRv26ETLXNIv5BPad84Buj7d3t9drquuWyy6sJ8OVKyynC7ZrWvntCYV05UdwauRqJ-Oj5s7jHBcdgH0rSemnHFVmzXqmZYZiC_RorP1GIfM75Xqw6gwIQhI5qvEOkv_yqtoRk3YLk-9S13Pwu3HA8eCnsiR73m0AaIeaLDbA5qYqg/https%3A%2F%2Fbrainweb.bic.mni.mcgill.ca%2Fanatomic_normal_20.html) . After i run recon-all, freesurfer ends without any error in 4 seconds. ## >recon-all -i $data_dir/$i/mT1t.nii.gz -sd $rdir/results/freesurfer -s $i Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /results/freesurfer Actual FREESURFER_HOME /FreeSurfer/freesurfer-linux-centos8_x86_64-7.1.1 mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz reading from /data/subject54_t1w_p4/mT1t.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz... @#@FSTIME 2021:08:25:16:50:08 mri_convert N 2 e 3.56 S 0.08 U 2.84 P 82% M 53580 F 0 R 12154 W 0 c 1228 w 1454 I 83632 O 83736 L 3.30 2.59 1.96 @#@FSLOADPOST 2021:08:25:16:50:12 mri_convert N 2 3.27 2.59 1.97 /results/freesurfer/subject54_t1w_p4/mri/transforms /results/freesurfer/subject54_t1w_p4 /results/freesurfer/subject54_t1w_p4 Started at Mi 25. Aug 16:50:07 CEST 2021 Ended at Mi 25. Aug 16:50:13 CEST 2021 #@#%# recon-all-run-time-hours 0.002 recon-all -s subject54_t1w_p4 finished without error at Mi 25. Aug 16:50:13 CEST 2021 done ## Please help! Thanks! [image: image.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all ends in 4 seconds without error!!
External Email - Use Caution haha. Thanks, works. On Wed, Aug 25, 2021 at 7:49 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > That must be a record! > > Seriously speaking: try adding -all to the command; I guarantee it won’t > take 4 seconds this time :-P > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1Q9HyXagUyT4lCMcetbg6yt7AnWPT9pldyicLP8-uK13t8fkXdETMILEHXdDAGz7qNgK8MBIkcb8HLpqYV-oxewpPioG_EspLQVYYhLHfLOvPXk3vSbb5DVJ6nRs2V4QwQZXulUxg2M2_GqOROHWi-TB9KyiBcPWmc4JGUIhhIGtJ6o3uCFNb6kCnhApPYc-Y4O-LPm1SacVHfhu2Ed2QzkGUtwgxu8u5MqaBpajJz7zSqpwpiURhxidPnsAAQhOMyMO5-qsvqwIExnTA9maNlw/http%3A%2F%2Fwww.jeiglesias.com > > On Aug 25, 2021, at 12:04, vin rasa wrote: > > External Email - Use Caution > > Dear Freesurfer Experts, > Greetings! > > I am trying to run freesurfer on Synthetic T1 data (see in snapshot: > *''Simulated > T1 image', last sentence in the snapshot*') from Brainweb (*MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" claiming > to be* > https://secure-web.cisco.com/1jlTJcPH2Z123dCmKJ2XGWu2qwl-BatM3mCIgVhwsiDIyhb8whhhtTEsew8YqgTo4wjLkuH1qKETfILsqQg7bVld1BfOTeDAux8zhhQzqPe1mH0Ce_Z46Z7ifN0gGAOUYc6aJgG80D5zV5nwAof8-41A0fdPo91POBTPr6BfkI8xI5wCQECTdjzjjYK_EPQXcQZRR_jtcFrgf9LG6ns_IK355o-18iv-JAVf2RtVDHWkLIxbjnsulDpZDC9RQ2vq8OR1rQ89xS4A_BUDsdaXCcA/https%3A%2F%2Fbrainweb.bic.mni.mcgill.ca%2Fanatomic_normal_20.html > <https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6dr5d7BqISQ4OX0IXN53ZgfgLg7fOkHGB7XNRBVvnJnU9CE4TEtRcWizxFRY_pRv26ETLXNIv5BPad84Buj7d3t9drquuWyy6sJ8OVKyynC7ZrWvntCYV05UdwauRqJ-Oj5s7jHBcdgH0rSemnHFVmzXqmZYZiC_RorP1GIfM75Xqw6gwIQhI5qvEOkv_yqtoRk3YLk-9S13Pwu3HA8eCnsiR73m0AaIeaLDbA5qYqg/https%3A%2F%2Fbrainweb.bic.mni.mcgill.ca%2Fanatomic_normal_20.html>) > . > > After i run recon-all, freesurfer ends without any error in 4 seconds. > > > ## > >recon-all -i $data_dir/$i/mT1t.nii.gz -sd $rdir/results/freesurfer -s $i > > Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 > Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 > INFO: SUBJECTS_DIR is /results/freesurfer > Actual FREESURFER_HOME /FreeSurfer/freesurfer-linux-centos8_x86_64-7.1.1 > > mri_convert /data/subject54_t1w_p4/mT1t.nii.gz > /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz > mri_convert /data/subject54_t1w_p4/mT1t.nii.gz > /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz > reading from /data/subject54_t1w_p4/mT1t.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz... > @#@FSTIME 2021:08:25:16:50:08 mri_convert N 2 e 3.56 S 0.08 U 2.84 P 82% > M 53580 F 0 R 12154 W 0 c 1228 w 1454 I 83632 O 83736 L 3.30 2.59 1.96 > @#@FSLOADPOST 2021:08:25:16:50:12 mri_convert N 2 3.27 2.59 1.97 > /results/freesurfer/subject54_t1w_p4/mri/transforms > /results/freesurfer/subject54_t1w_p4 > /results/freesurfer/subject54_t1w_p4 > > Started at Mi 25. Aug 16:50:07 CEST 2021 > Ended at Mi 25. Aug 16:50:13 CEST 2021 > #@#%# recon-all-run-time-hours 0.002 > recon-all -s subject54_t1w_p4 finished without error at Mi 25. Aug > 16:50:13 CEST 2021 > done > ## > > Please help! > > Thanks! > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/17QYxP1UcRXp_uuW5xKORvDs2Z7vX5x0OJjypIlggHJWn45EmuVOzPhbk1OKn0kBjH4FnFIo9kHWk5PXh3Qerh71rqIisSKPzKnvuUK-5L7zBxX0YYdSUJWd7Fz1IDZIkKW8L8uj4gk0U_Ks0V793N2rLGI4VrNJKjLP8R0oLkWVjunqU7LspvM89zghlfhKitNcNAMWAHu_ecocPPMbf18OLcV9F4seuB3eURBysNrXJhPqJexVGRZZ8HxApWHUErhf2J-B4E9JHWNHsXCxQfA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > 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 Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1Owmy2DujkCvlVfpkSze6Ieerxe9BNG_ZTKVsEBRcjUYPmkGjm3urytxIhNPBzjG3ZZQpO-xpNY1gwd54VyAUtbXOSHs-2zY_MSK8Bfct-VLhzu9U69SJ-n0XsJjIXD3EROLea4DOgqZjwjSl7DN5DT2F8JbkLRI61kjji9MBNaX9WvyzPwknTz7_7pm62rBVybDCQlzcGkdq6UZ2mMxbZUcR1gPVEiZmH-4nl_QIbv8m6eLtUK3lEHWTpMd341p947wwNdI47no_DBZXUDUxVA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. > > Please note that this e-mail is not secure (encrypted).
