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 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.
