The problem is that you are using the wrong segmentation number for left insula. You used 19, which is reasonable given that FreeSurferColorLUT.txt lists that as left insula, but the one you want is actually 1035.
doug On 08/12/2015 11:09 AM, Gay,Charles Wysaw wrote: > Hi Doug - > Here is some of the information: > FREESURFER_HOME: > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Kernel info: Darwin 14.0.0 x86_64 > > --------------------------------------------------------------------- > Please include the following additional information in your report: > > 1) subject name: B113v1 > 2) the entire command-line executed: > [phhp-chazgay-mb:Bishop/FreeSurfer_R01/Project] chaz.gay% fcseed-sess > -s B113v1 -cfg mean.L_Insula.config > 3) the error message generated: see below - > 4) optionally include the subject's /script/recon-all.log: attached. > 5) SUBJECTS_DIR: > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects > > Logfile is > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/log/fcseed-sess.L_Insula.dat.log.B113v1 > Wed Aug 12 11:03:33 EDT 2015 > Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: > Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 > setenv SUBJECTS_DIR > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects > cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess > > > -s B113v1 -cfg mean.L_Insula.config > freesurfer-Darwin-lion-stable-pub-v5.3.0 > Wed Aug 12 11:03:33 EDT 2015 > Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: > Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 > setenv SUBJECTS_DIR > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects > cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess > > > -s B113v1 -cfg mean.L_Insula.config > freesurfer-Darwin-lion-stable-pub-v5.3.0 > > mri_label2vol --seg > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/B113v1/mri/aparc+aseg.mgz > > --reg > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat > > --temp > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz > > --fillthresh .5 --o > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz > > --pvf > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz > PVF > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz > Number of labels: 0 > Annot File: (null) > Template Volume: > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz > Outut Volume: > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz > Registration File: > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ > Template RAS-to-Vox: -------- > -0.333 0.000 0.000 40.000; > -0.000 -0.000 -0.333 40.000; > -0.000 0.333 -0.000 19.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 27 > nHits Thresh: 13.5 > Loading registration from > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat > RegMat: -------- > 1.000 -0.011 -0.001 9.758; > -0.002 -0.246 0.969 -27.653; > 0.011 0.969 0.246 -1.912; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -0.333 0.004 0.000 36.747; > -0.004 -0.323 -0.082 40.637; > -0.001 -0.082 0.323 9.782; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > ASeg2Vol: Sorting > ASeg2Vol: Mapping > ASeg2Vol: Reverse Map > nmisses = 234 (0 filled) > ASeg2Vol: done > PVF > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz > Computing PVF 27 > mri_binarize --i > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz > > --o > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > > --match 19 > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project > cmdline mri_binarize --i > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz > > --o > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > > --match 19 > sysname Darwin > hostname phhp-chazgay-mb.ad.ufl.edu > machine x86_64 > user chaz.gay > > input > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz > frame 0 > nErode3d 0 > nErode2d 0 > output > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > Binarizing based on matching values > nMatch 1 > 0 19 > binval 1 > binvalnot 0 > Found 0 values in range > Counting number of voxels > Found 0 voxels in final mask > mri_binarize done > mri_segstats --i > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz > > --seg > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > > --id 1 --sum > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/junk.sum > > --avgwfvol > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --i > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz > > --seg > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > > --id 1 --sum > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/junk.sum > > --avgwfvol > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh > sysname Darwin > hostname phhp-chazgay-mb.ad.ufl.edu > machine x86_64 > user chaz.gay > UseRobust 0 > Loading > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz > Loading > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz > Voxel Volume is 27 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0.000 > MRIalloc(0, 1, 1): bad parm > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to > /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh > Segmentation fault > > On Wed, 12 Aug 2015 10:40:14 -0400, Douglas N Greve wrote: >> Hi Chaz, we'll need more info. Please see >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> On 08/11/2015 11:40 PM, Gay,Charles Wysaw wrote: >>> I've completed steps 1 thru 4 successfully (i think). When I run the >>> fcseed-sess with the segid for the left insula I'm getting an >>> segmentation fault. I've tried both segids 11117 and 19 and have the >>> same result. Selecting other seed regions (left posterior cingulate) >>> generates a 1d file timecourse. >>> the error log was the same both times: >>> MRIalloc(0, 1, 1): bad parm >>> Any ideas on what to do? >>> Thanks >>> Chaz >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> -- >> 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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
