Hi, I am experiencing the same problem. When I try to do the motion correction on fmri data it stops with a segmentation fault in mri_convert. This used to work until this week.
Best Marcus On 13.05.2011 12:48, Chindhuri Selvadurai wrote: > Hi all, > > We are trying to run individual analyses on several subjects, and we keep > getting a 'Segmentation Fault.' We have run other subjects with the same > command a while ago, and the command worked fine at that time. Do you > have any idea what would be causing this error? The output is included > below: > > Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 > Subjects Dir: /cluster/manoach/milton/subjects > FreeSurfer v. Stable 5 > > > Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 ---------------- > Fri May 13 12:21:58 EDT 2011 > Run: 012 ---------------- > Fri May 13 12:21:58 EDT 2011 > Update not needed > Fri May 13 12:21:58 EDT 2011 > register-sess completed > PBMCT15 MC ----------------------------- > mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d > /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run > -nolog -update > Logfile is /dev/null > ------------------------------------------- > /autofs/cluster/manoach/milton/subjects/PBMCT15 > RunList: 012 > ------- ************************** ----------- > ------- Motion Correcting Run 012 ----------- > ------- ************************** ----------- > sess = PBMCT15 > Fri May 13 12:21:58 EDT 2011 > mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat > 012/fmcpr.mcdat > /autofs/cluster/manoach/milton/subjects/PBMCT15/bold > mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii > log file is 012/fmcpr.nii.gz.mclog > mcdat file is 012/fmcpr.mcdat > tmp dir is 012/tmp.mc-afni2.3377 > #@# -------------------------------- > /autofs/cluster/manoach/milton/subjects/PBMCT15/bold > mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip > 0 --ndrop 0 -odt float > mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip > 0 --ndrop 0 -odt float > nskip = 0 > ndrop = 0 > $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ > reading from 012/template.nii... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998297, -0.0395807, 0.0428535) > j_ras = (0.0411249, -0.998513, 0.0357732) > k_ras = (0.0413739, 0.0374746, 0.998441) > changing data type from short to float (noscale = 0)... > writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... > #@# -------------------------------- > /autofs/cluster/manoach/milton/subjects/PBMCT15/bold > mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float > mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float > Segmentation fault > > > Thanks! > > Best, > > Chindhuri Selvadurai > > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > _______________________________________________ > 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 . 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.
