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 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.
