Hi Doug, It is writing to the trumpet directory which is not full. It does write out the output file aparc.annot.ctab, but seg faults at the end.
Here is the df -h output for the trumpet directory (775Gb are available): [jdr...@trumpet label]$ df -h Filesystem Size Used Avail Use% Mounted on /dev/md2 50G 7.7G 40G 17% / /dev/md3 862G 43G 775G 6% /trumpet /dev/md0 122M 21M 95M 19% /boot tmpfs 3.0G 952K 3.0G 1% /dev/shm nil:/people/j 185G 180G 3.1G 99% /people/j nil:/scratch 62G 60G 1.1G 99% /scratch nil:/irus 40G 38G 2.0G 95% /net/nil/irus nil:/local 40G 38G 2.0G 95% /localaparc.annot.ctab The subject is not an average subject but is part of an Alzheimer's study. I have not done any manual interventions/corrections in freesurfer (maybe I should at this stage). I am just running the commands for a first try. Thanks, john On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Can you verify that the disk it is writing to is not full? > > Is this an average subject? > > doug > > John Drozd wrote: > >> Hello again, >> >> Sorry, I forgot to include the required info: >> >> john >> >> FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >> >> RedHat release: Fedora release 10 (Cambridge) >> >> Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >> >> --------------------------------------------------------------------- >> Please include the following additional information in your report: >> >> 1) subject name: convertedfile >> >> 2) the entire command-line executed: >> mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a >> ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh >> >> 3) the error message generated: >> Segmentation fault >> >> 4) optionally include the subject's /script/recon-all.log >> >> >> On Tue, May 26, 2009 at 2:23 PM, John Drozd <john.dr...@gmail.com<mailto: >> john.dr...@gmail.com>> wrote: >> >> Hello, >> >> I am running the reconall steps individually for a firts try. >> >> I noticed that I get a segmentation fault when I run >> mris_anatomical_stats as whown below: >> >> [jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f >> ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf >> ../label/aparc.annot.ctab convertedfile lh >> INFO: assuming MGZ format for >> volumes. computing >> statistics for each annotation in ../label/lh.aparc.annot. >> reading volume >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... >> reading input surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >> reading input pial surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... >> reading input white surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >> reading colortable from annotation file... >> colortable with 35 entries read (originally >> >> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> Saving annotation colortable ../label/aparc.annot.ctab >> >> table columns are: >> number of vertices >> total surface area (mm^2) >> total gray matter volume (mm^3) >> average cortical thickness +- standard deviation (mm) >> integrated rectified mean curvature >> integrated rectified Gaussian curvature >> folding index >> intrinsic curvature index >> structure name >> >> Segmentation fault >> >> john >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >
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