Hi Doug, So I just tried making my ROI a little bit bigger in an earlier binarizing step that created my segmentation, and when I ran fcseed-config and fcseed-sess in this same subject it ran without error. I guess it was a sizing issue! Let me know if you have any additional thoughts.
Thanks again for your help! Best, Alex > I actually already tried rerunning fcseed-config and fcseed-sess lowering > the fillthresh (even brought it down to 0) and I still got the same error. > I just tried .05 to be thorough but no dice :( > >> Try lowering the fillthreshold to .1 in fcseed-config (means you have to >> re-run fcseed-sess for all subjects, but see if it makes those two work). For such a small seed, it may even be better to use .05. On 05/21/2015 11:42 AM, Alexandra Tanner wrote: >>> The voxel size for this functional sequence is 3x3x3mm >>>> 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/ >> -- >> 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 > > > _______________________________________________ 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 . 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