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) _______________________________________________ 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. 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