Hi Doug,
I fixed the problem. i had given the path ../stats when I should have used ./stats.
Now it works:
[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
11531 7108 11411 1.451 1.619 0.114 0.089 366 37.0 unknown 1295 891 2178 2.425 0.532 0.117 0.028 11 1.6 bankssts 974 704 1943 2.590 0.832 0.154 0.042 19 1.8 caudalanteriorcingulate
3260 2212 5748 2.385 0.505 0.125 0.049 55 8.0 caudalmiddlefrontal
1872 1196 2383 1.811 0.445 0.147 0.051 28 4.0 cuneus 693 467 2361 3.584 0.791 0.147 0.088 15 2.6 entorhinal 4796 3279 9604 2.589 0.699 0.147 0.053 90 9.8 fusiform 6161 4063 10836 2.339 0.646 0.137 0.052 92 11.4 inferiorparietal 5067 3375 10530 2.586 0.756 0.152 0.064 118 13.1 inferiortemporal 1081 705 1860 2.360 0.767 0.153 0.063 22 2.6 isthmuscingulate 9902 6468 15926 2.218 0.616 0.158 0.063 184 23.8 lateraloccipital 3797 2613 7013 2.505 0.749 0.159 0.113 246 9.2 lateralorbitofrontal 3856 2526 5376 1.978 0.679 0.155 0.071 163 11.9 lingual 2341 1578 3433 2.080 0.657 0.134 0.038 35 4.0 medialorbitofrontal 4354 2924 9107 2.554 0.666 0.144 0.046 78 8.0 middletemporal 769 504 1623 2.774 0.850 0.113 0.035 8 1.0 parahippocampal 2055 1262 3268 2.334 0.684 0.112 0.038 31 3.8 paracentral 2055 1402 3801 2.422 0.485 0.125 0.034 25 2.9 parsopercularis 1020 701 1920 2.208 0.573 0.177 0.076 25 3.7 parsorbitalis 1792 1213 2899 2.136 0.498 0.126 0.035 23 2.7 parstriangularis 2111 1441 2038 1.504 0.381 0.158 0.067 34 6.2 pericalcarine 6149 3918 7916 1.801 0.569 0.115 0.037 73 9.4 postcentral 1685 1152 3253 2.559 0.744 0.175 0.072 45 5.2 posteriorcingulate 7186 4460 12819 2.523 0.621 0.112 0.040 91 10.8 precentral 4656 3134 7658 2.347 0.599 0.141 0.041 63 7.7 precuneus 981 704 2271 2.797 0.920 0.174 0.080 25 3.1 rostralanteriorcingulate 8129 5573 13843 2.126 0.559 0.146 0.052 147 16.5 rostralmiddlefrontal 10613 7339 19998 2.361 0.608 0.134 0.044 150 17.1 superiorfrontal 10405 6830 17061 2.194 0.647 0.133 0.038 138 15.6 superiorparietal 5177 3505 10352 2.580 0.610 0.119 0.054 58 6.5 superiortemporal 5240 3516 9413 2.368 0.520 0.136 0.093 293 9.9 supramarginal 342 235 766 2.442 0.556 0.203 0.082 12 1.3 frontalpole 667 458 2300 3.769 0.639 0.143 0.049 9 1.4 temporalpole 679 385 913 2.282 0.333 0.124 0.047 7 1.1 transversetemporal
Thanks for all your help.
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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In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- 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