It looks like you are using the dev environment? I fixed this problem a couple of days ago, but it must not have propagated into dev. Why are you using dev? doug
On 7/25/12 2:02 PM, Yigal Agam wrote: > Hi, > > We're getting the following error from recon-all: > > command line: > > pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i > /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-000015-000001.dcm > -mail etan...@nmr.mgh.harvard.edu' > > output: > > > ... > > ... > > mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o > ./tmp.mri_nu_correct.mni.14699/ones.mgz > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /autofs/cluster/manoach/dod/subjects/DODASD012/mri > cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 > --o ./tmp.mri_nu_correct.mni.14699/ones.mgz > sysname Linux > hostname compute-0-88 > machine x86_64 > user etanski > > input ./tmp.mri_nu_correct.mni.14699/nu2.mnc > frame 0 > nErode3d 0 > nErode2d 0 > output ./tmp.mri_nu_correct.mni.14699/ones.mgz > Binarizing based on threshold > min -1 > max +infinity > binval 1 > binvalnot 0 > Found 16777216 values in range > Counting number of voxels > Found 16777216 voxels in final mask > mri_binarize done > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i > orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.14699/input.mean.dat > > $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz > --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.14699/input.mean.dat > sysname Linux > hostname compute-0-88 > machine x86_64 > user etanski > Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz > Loading orig.mgz > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.14699/input.mean.dat > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i > ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.14699/output.mean.dat > > $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz > --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.14699/output.mean.dat > sysname Linux > hostname compute-0-88 > machine x86_64 > user etanski > Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz > Loading ./tmp.mri_nu_correct.mni.14699/nu2.mnc > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.14699/output.mean.dat > (standard_in) 1: syntax error > mris_calc -o ./tmp.mri_nu_correct.mni.14699/nu2.mnc > ./tmp.mri_nu_correct.mni.14699/nu2.mnc mul > Linux compute-0-88 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 > BST 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s DODASD012 exited with ERRORS at Wed Jul 25 12:27:28 EDT 2012 > > For more details, see the log file > /autofs/cluster/manoach/dod/subjects/DODASD012/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Any suggestions? > > Thanks, > Yigal > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.
