What is the voxel size of your functional? 54 is small, but I would expect it to still work.
On 05/21/2015 11:20 AM, Alexandra Tanner wrote: > 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/ >> >> >> > > > -- 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. 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