Hi Doug,
./stats/lh.aparc.stats does NOT exist, but it still seg faulted when I have chmod'd -R 777 the mri directory recursively.
john
On Tue, May 26, 2009 at 3:43 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Does ../stats/lh.aparc.stats exist and do you have write perms to the file and directory?
John Drozd wrote:
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):
[jdrozd@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 < greve@nmr.mgh.harvard.edu mailto:greve@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.drozd@gmail.com <mailto:john.drozd@gmail.com> <mailto:john.drozd@gmail.com <mailto:john.drozd@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: [jdrozd@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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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