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: B113v12) 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 2015Darwin 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 2015Darwin 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-v5.3.0mri_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 0setenv 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: 13.5Loading 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: donePVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz
Computing PVF 27mri_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/Projectcmdline 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.gayinput /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz
frame 0 nErode3d 0 nErode2d 0output /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 donemri_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 $ cwdcmdline 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 0Loading /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 frameWriting 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.htmlOutgoing: 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/freesurferThe 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-mailcontains 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.
recon-all-status.log
Description: Binary data
_______________________________________________ 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.
