I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at
/cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: > Hi Doug and Freesurfers, > > I'm running fcseed-sess to compute the time course in 12 different ROIs > (created with fcseed-config) across 27 subjects. I'm having an issue, > however, where fcseed-sess completes for a particular ROI in most subjects > but errors out for a few subjects (see log below). I saw someone had the > same issue in the mail archives > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) > so I checked the registration but everything seems to look fine. Any other > suggestions on how to fix this issue would be greatly appreciated! > > Thanks! > Alex > > > fcseed-config and fcseed-sess commands/logs: > > # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg > /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg > -segid 1 -seg > lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz > -fcname > lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd > resting -mean -force > # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun > # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ > # Wed May 20 14:03:50 EDT 2015 > > fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat > fsd resting > segstem > lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol > RegDOF 6 > FillThresh .5 > DoMean 1 > DoSVD 0 > DoSqr 0 > MakeMask 0 > WMErode 0 > SVDSynth 0 > DoWM 0 > UseB0DC 0 > segidlist 1 > > > > Tue May 19 17:40:27 EDT 2015 > Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC > 2014 x86_64 x86_64 x86_64 GNU/Linux > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun > cd /autofs/cluster/roffman/users/Stable5_PerRun > /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess > -s NNC0931 -cfg > /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg > freesurfer-Linux-centos6_x86_64-dev-20150519 > > mri_label2vol --seg > /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz > --reg > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta > --temp > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii > --fillthresh .5 --o > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii > --pvf > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii > PVF > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii > Number of labels: 0 > Annot File: (null) > Template Volume: > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii > Outut Volume: > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii > Registration File: > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 0 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun > $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ > Template RAS-to-Vox: -------- > -0.33333 -0.00000 -0.00000 36.00000; > -0.00000 -0.00000 -0.33333 36.00000; > -0.00000 0.33333 -0.00000 23.50000; > -0.00000 -0.00000 -0.00000 1.00000; > Template Voxel Volume: 27 > nHits Thresh: 13.5 > Loading registration from > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta > regio_read_register: loading lta > RegMat: -------- > 0.99848 0.02007 -0.05128 -0.41633; > 0.04918 0.09388 0.99437 -30.67201; > -0.02477 0.99538 -0.09275 5.35657; > 0.00000 0.00000 0.00000 1.00000; > Label RAS-to-Vox: -------- > -0.33283 -0.00669 0.01709 36.13877; > 0.00826 -0.33179 0.03092 34.21448; > 0.01639 0.03129 0.33146 13.27600; > 0.00000 0.00000 0.00000 1.00000; > PVF > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii > Computing PVF 27 > mri_label2vol done > mri_binarize --i > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii > --o > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > --match 1 > > $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ > cwd /autofs/cluster/roffman/users/Stable5_PerRun > cmdline mri_binarize --i > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii > --o > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > --match 1 > sysname Linux > hostname dauntless > machine x86_64 > user atanner > > input > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii > frame 0 > nErode3d 0 > nErode2d 0 > output > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > Binarizing based on matching values > nMatch 1 > 0 1 > binval 1 > binvalnot 0 > fstart = 0, fend = 0, nframes = 1 > Found 0 values in range > Counting number of voxels in first frame > Found 0 voxels in final mask > Count: 0 0.000000 243648 0.000000 > mri_binarize done > mri_segstats --i > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/fmcpr.nii > --seg > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > --id 1 --sum > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/junk.sum > --avgwfvol > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/avgwf.mgh > > $Id: mri_segstats.c,v 1.113 2015/05/05 22:32:40 nicks Exp $ > cwd > cmdline mri_segstats --i > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/fmcpr.nii > --seg > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > --id 1 --sum > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/junk.sum > --avgwfvol > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/avgwf.mgh > sysname Linux > hostname dauntless > machine x86_64 > user atanner > UseRobust 0 > Loading > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > Loading > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/fmcpr.nii > Voxel Volume is 27 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > > Reporting on 0 segmentations > Using PrintSegStat > Computing spatial average of each frame > > Writing to > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/avgwf.mgh > Segmentation fault (core dumped) > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
