Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size?
Thanks! Alex > 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.
