Hi Doug,
I fixed the problem. i had given the path ../stats when I should have used
./stats.
Now it works:
[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
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
<gr...@nmr.mgh.harvard.edu>wrote:
> 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):
>>
>> [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 <mailto: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>
>> <mailto: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
>> <mailto: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 <mailto: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
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>
>>
>>
>>
> --
> 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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