[Freesurfer] trac-all error (segmentation fault?)
Hi Freesurfer experts, I tried running trac-all with my config file and received the following error : Segmentation fault Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33 UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Tue Jun 24 11:15:12 EDT 2014 Any help would be greatly appreciated! I am attaching the config file, log and error files. Thank you! Durai Tue Jun 24 11:15:10 EDT 2014 /home/owner/data_bkup /home/owner/Desktop/freesurfer/bin/trac-all -c 2_dmrirc.bnst -prep -bedp -path Subject wzp102 SUBJECTS_DIR /home/owner/data_bkup FREESURFER_HOME /home/owner/Desktop/freesurfer Actual FREESURFER_HOME /home/owner/Desktop/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 owner 129-2-36-232 Linux 129-2-36-232 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33 UTC 2013 (5f00a32) 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 95651 maxlocks unlimited maxsignal95651 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 12261560 100681082193452 0 6460966565336 -/+ buffers/cache:28566769404884 Swap: 16472056 274404 16197652 Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/24-15:15:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: owner Machine: 129-2-36-232 Platform: Linux PlatformVersion: 3.4.33-2.24-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/24-15:15:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: owner Machine: 129-2-36-232 Platform: Linux PlatformVersion: 3.4.33-2.24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/24-15:15:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: owner Machine: 129-2-36-232 Platform: Linux PlatformVersion: 3.4.33-2.24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/24-15:15:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: owner Machine: 129-2-36-232 Platform: Linux PlatformVersion: 3.4.33-2.24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/24-15:15:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: owner Machine: 129-2-36-232 Platform: Linux PlatformVersion: 3.4.33-2.24-desktop CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/owner/Desktop/freesurfer Previous: /cell_root/software/freesurfer/new/sys New invocation of trac-paths owner 129-2-36-232 Linux 129-2-36-232 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33 UTC 2013 (5f00a32) 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 95651 maxlocks unlimited maxsignal95651 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 12261560 100680122193548 0 6460966565360 -/+ buffers/cache:28565569405004 Swap: 16472056 274404 16197652 #- /home/owner/Desktop/freesurfer/bin/trac-paths #- #@# Path reconstruction Tue Jun 24 11:15:12 EDT 2014 rm -rf /home/owner/data_bkup/wzp102/dpath/lh.unc_AS_avg33_mni_flt rm -rf /home/owner/data_bkup/wzp102/dpath/rh.unc_AS_avg33_mni_flt /home/owner/Desktop/freesurfer/bin/dmri_paths --outdir /home/owner/data_bkup/wzp102/dpath/lh.unc_AS_avg33_mni_flt /home/owner/data_bkup/wzp102/dpath/rh.unc_AS_avg33_mni_flt --dwi /home/owner/data_bkup/wzp102/dmri/dwi.nii.gz --grad /home/owner/data_bkup/wzp102/dmri/bvecs --bval /home/owner/data_bkup/wzp102/dmri/bvals --mask /home/owner/data_bkup/wzp102/dlabel/diff/lowb_brain_mask.nii.gz --bpdir /
[Freesurfer] recon-all mri_nu_correct error
Hi Freesurfer experts, I was running recon-all on a cluster and encountered the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov 11 03:23:58 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s hcp80100307 exited with ERRORS at Wed May 21 12:43:36 EDT 2014 Any idea whats the source of the error? Thanks! On Wed, May 21, 2014 at 2:20 PM, C.P. Frost wrote: > Hello all, > > My site has recently upgraded to the newest version of Freesurfer, and > I've run a set of subjects on recon-all using the hippocampal subfield > segmentation flag. Everything went well. Then in running > kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages > indicating that certain expected files didn't exist. > > In particular, among output files labeled with the scheme > $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and > ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz > -- in other words, the script expected a hyphen but instead the filenames > contained an underscroe. > > After renaming the files appropriately, kvlQuantify... successfully > generated the nonPartialVolumeStats files and everything worked fine. > > I didn't see any threads with this solution, and only one or two that > mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it > up in case it could be addressed in a future release. > > Cheers, > C.P. Frost > > ___ > 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 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] SEEDING in Tracula
Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts. However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc? I guess I am asking if it can do LOCAL tractography of any kind? Thank you! ___ 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] recon-all subject folder size
Hi Freesurfer experts, I am successfully running recon-all on my cluster. However I find that the subject folders have sizes ranging from 300mb to 900mb. I grepped all recon-all.log files for "finished without error" and that seemed fine for all subjects. But I would like to know what is the expected subject folder size when you run recon-all (with -all option) starting from a standard MPRAGE T1 image. This might be useful since I have limited control over the cluster nodes where the processing takes place. Thank you Durai On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan wrote: > Hi Freesurfer experts, > > so I got this error when I ran recon-all on my cluster. I am really hoping > this is just a case of missing GCC libraries and nothing is wrong with the > Freesurfer installation on the nodes. Kindly confirm this. > > Thank you > > > ** > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /** > Actual FREESURFER_HOME /** > Linux * SMP Fri Mar 22 05:41:51 EDT 2013 > x86_64 x86_64 x86_64 GNU/Linux > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_convert) > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_convert) > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_convert) > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by tkregister2_cmdl) > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by tkregister2_cmdl) > tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by tkregister2_cmdl) > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_make_uchar) > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_make_uchar) > mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_make_uchar) > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_normalize) > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_normalize) > mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_normalize) > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_watershed) > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_watershed) > mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_watershed) > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_gcut) > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_gcut) > mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_gcut) > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_segment) > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_segment) > mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_segment) > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_label2label) > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_label2label) > mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_label2label) > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_em_register) > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_em_register) > mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_em_register) > mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_ca_normalize) > mri_ca_normalize: /usr/lib64/li
[Freesurfer] Which is broken - GCC or Freesurfer build?
Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you ** Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /** Actual FREESURFER_HOME /** Linux * SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register) mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_label) mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_label) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_pretess) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_pretess) mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_pretess) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fil
