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
Hi Chinduri, is this still happening? I can't replicate.
doug
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
Not happening anymore, thanks!
Hi Chinduri, is this still happening? I can't replicate.
doug
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307
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
OK, I've verified and fixed this. It will be in dev in the next build (probably overnight). Are you using dev? doug
Marcus Belke wrote:
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
freesurfer@nmr.mgh.harvard.edu
-
Chindhuri Selvadurai -
Douglas N Greve -
Marcus Belke