Re: [Freesurfer] Petsurfer mri_gtmpvc error
I think you are probably exceeding the memory limit of your compute (just that matrix takes 9G) On 03/28/2017 03:53 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: > Thanks for the response. I ran the command again with FWHM 6, but am getting > a 'MatrixAlloc(2368,100): allocation failed' error. > > mri_gtmpvc --i OutBrick_run_008.nii --reg template.reg.lta --psf 6 --seg > gtmseg.mgz --default-seg-merge --o gtmpvc.output > > This is the output log file- > $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ > setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects > cd /home/agrawals8/freesurfer/subjects/NIH047 > mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 > --seg mri/gtmseg.mgz --default-seg-merge --o gtmpvc.output > sysname Linux > hostname ndsw-eeg-dreifuss.ninds.nih.gov > machine x86_64 > user agrawals8 > vgthresh 0.001000 > nReplace 18 > 0. 0. 0. 0. 0. 0. > Loading seg for gtm mri/gtmseg.mgz > Loading ctab mri/gtmseg.ctab > Reading mri/gtmseg.lta > Data load time 24.9 sec > nmask = 2368, nsegs = 100, excluding segid=0 > FWHM: 6 6 6 > Std: 2.54797 2.54797 2.54797 > nPad 13, PadThresh 0.0001 > Segmentations used for rescaling > 174 Pons > MEM: Size 479268 Peak: 956464 RSS: 339992 Data: 338176 Stk: 92 > MEM: Size 10095992 Peak: 10095992 RSS: 969132 Data: 9954900 Stk: 92 > MEM: Size 10189788 Peak: 10190808 RSS: 1062848 Data: 10048696 Stk: 92 > > System specs for this computer- CentOS 6.7, 7 Processors- Intel Xeon CPU > @2.2GHZ, Memory 11GB, Available disk space 419 GB. > > Regards > Shubhi > > From: freesurfer-requ...@nmr.mgh.harvard.edu > [freesurfer-requ...@nmr.mgh.harvard.edu] > Sent: Thursday, March 23, 2017 10:08 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 157, Issue 61 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Petsurfer mri_gtmpvc error (Douglas Greve) > 2. Re: contrast between two independent CTh maps? >(Uquillas, Federico D'Oleire) > 3. Re: A Bug in Monte-Carlo Simulation. (Douglas Greve) > 4. Re: Qdec 1.5 (Douglas Greve) > 5. Re: Fw: PETsurfer surface based analysis (miracoo...@gmail.com) > 6. Re: LME mass univariate model (Bronwyn Overs) > 7. Re: Qdec 1.5 (Duy Nguyen) > 8. Correcting Skull-Strip Errors - Watershed Algorithm Question >(Abhinav Kurada) > 9. Petsc Error in Freesurfer v6.0 (Michael ONeill) >10. Re: Thickness asymmetry and LH/RH corresponding vertices in >fsaverage (Dorian P.) > > > -- > > Message: 1 > Date: Wed, 22 Mar 2017 17:11:49 -0400 > From: Douglas Greve > Subject: Re: [Freesurfer] Petsurfer mri_gtmpvc error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <7422f5df-b0e5-587b-d71c-7dd2cc14a...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > FWHM should be the impulse response FWHM for your scanner. This is a > number (eg, the HR+ is about 6), not the string 'FWHM' > > > On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: >> Hi, >> I am trying to run SGTM partial volume correction in Petsurfer by >> following the tutorial on the wiki. Every step preceding mri_gtmpvc >> has been successful and the coregistration looks good. >> the last step, mri_gtmpvc command gives an error- >> Segmentation fault (core dumped) >> >> This is the information from the log file- >> >> $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ >> setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects >> cd /home/agrawals8/freesurfer/subjects/NIH047 >> mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta >> --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 >> --o gtmpvc.output >> sysname Linux >> hostname ndsw-eeg-dreifuss.ninds.nih.gov >> machine x86_64 >> user agrawals8 >> vgthresh 0.001000 >> nReplace
Re: [Freesurfer] Petsurfer mri_gtmpvc error
Thanks for the response. I ran the command again with FWHM 6, but am getting a 'MatrixAlloc(2368,100): allocation failed' error. mri_gtmpvc --i OutBrick_run_008.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --o gtmpvc.output This is the output log file- $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects cd /home/agrawals8/freesurfer/subjects/NIH047 mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --o gtmpvc.output sysname Linux hostname ndsw-eeg-dreifuss.ninds.nih.gov machine x86_64 user agrawals8 vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta Data load time 24.9 sec nmask = 2368, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 13, PadThresh 0.0001 Segmentations used for rescaling 174 Pons MEM: Size 479268 Peak: 956464 RSS: 339992 Data: 338176 Stk: 92 MEM: Size 10095992 Peak: 10095992 RSS: 969132 Data: 9954900 Stk: 92 MEM: Size 10189788 Peak: 10190808 RSS: 1062848 Data: 10048696 Stk: 92 System specs for this computer- CentOS 6.7, 7 Processors- Intel Xeon CPU @2.2GHZ, Memory 11GB, Available disk space 419 GB. Regards Shubhi From: freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu] Sent: Thursday, March 23, 2017 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 61 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Petsurfer mri_gtmpvc error (Douglas Greve) 2. Re: contrast between two independent CTh maps? (Uquillas, Federico D'Oleire) 3. Re: A Bug in Monte-Carlo Simulation. (Douglas Greve) 4. Re: Qdec 1.5 (Douglas Greve) 5. Re: Fw: PETsurfer surface based analysis (miracoo...@gmail.com) 6. Re: LME mass univariate model (Bronwyn Overs) 7. Re: Qdec 1.5 (Duy Nguyen) 8. Correcting Skull-Strip Errors - Watershed Algorithm Question (Abhinav Kurada) 9. Petsc Error in Freesurfer v6.0 (Michael ONeill) 10. Re: Thickness asymmetry and LH/RH corresponding vertices in fsaverage (Dorian P.) -- Message: 1 Date: Wed, 22 Mar 2017 17:11:49 -0400 From: Douglas Greve Subject: Re: [Freesurfer] Petsurfer mri_gtmpvc error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <7422f5df-b0e5-587b-d71c-7dd2cc14a...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" FWHM should be the impulse response FWHM for your scanner. This is a number (eg, the HR+ is about 6), not the string 'FWHM' On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: > Hi, > I am trying to run SGTM partial volume correction in Petsurfer by > following the tutorial on the wiki. Every step preceding mri_gtmpvc > has been successful and the coregistration looks good. > the last step, mri_gtmpvc command gives an error- > Segmentation fault (core dumped) > > This is the information from the log file- > > $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ > setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects > cd /home/agrawals8/freesurfer/subjects/NIH047 > mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta > --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 > --o gtmpvc.output > sysname Linux > hostname ndsw-eeg-dreifuss.ninds.nih.gov > machine x86_64 > user agrawals8 > vgthresh 0.001000 > nReplace 18 > 0. 0. 0. 0. 0. 0. > Loading seg for gtm mri/gtmseg.mgz > Loading ctab mri/gtmseg.ctab > Reading mri/gtmseg.lta > MEM: Size 479268 Peak: 955936 RSS: 339984 Data: 338176 Stk: 92 > MEM: Size 570956 Peak: 955936 RSS: 431688 Data: 429864 Stk: 92 > Data load time 25.9 sec > nmask = 2680458, nsegs = 100, excluding segid=0 > FWHM: 6 6 6 > Std: 2.54797 2.54797 2.54797 > nPad 13, PadThresh 0.0001 > Segmentations used for rescaling > 174 Pons > MEM: Size 422356 Peak: 955936 RSS: 283024 Data: 281264 Stk: 92 > > > > ___ > Freesurfer mailing l
Re: [Freesurfer] Petsurfer mri_gtmpvc error
FWHM should be the impulse response FWHM for your scanner. This is a number (eg, the HR+ is about 6), not the string 'FWHM' On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: Hi, I am trying to run SGTM partial volume correction in Petsurfer by following the tutorial on the wiki. Every step preceding mri_gtmpvc has been successful and the coregistration looks good. the last step, mri_gtmpvc command gives an error- Segmentation fault (core dumped) This is the information from the log file- $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects cd /home/agrawals8/freesurfer/subjects/NIH047 mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 --o gtmpvc.output sysname Linux hostname ndsw-eeg-dreifuss.ninds.nih.gov machine x86_64 user agrawals8 vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta MEM: Size 479268 Peak: 955936 RSS: 339984 Data: 338176 Stk: 92 MEM: Size 570956 Peak: 955936 RSS: 431688 Data: 429864 Stk: 92 Data load time 25.9 sec nmask = 2680458, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 13, PadThresh 0.0001 Segmentations used for rescaling 174 Pons MEM: Size 422356 Peak: 955936 RSS: 283024 Data: 281264 Stk: 92 ___ 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.
[Freesurfer] Petsurfer mri_gtmpvc error
Hi, I am trying to run SGTM partial volume correction in Petsurfer by following the tutorial on the wiki. Every step preceding mri_gtmpvc has been successful and the coregistration looks good. the last step, mri_gtmpvc command gives an error- Segmentation fault (core dumped) This is the information from the log file- $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects cd /home/agrawals8/freesurfer/subjects/NIH047 mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 --o gtmpvc.output sysname Linux hostname ndsw-eeg-dreifuss.ninds.nih.gov machine x86_64 user agrawals8 vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta MEM: Size 479268 Peak: 955936 RSS: 339984 Data: 338176 Stk: 92 MEM: Size 570956 Peak: 955936 RSS: 431688 Data: 429864 Stk: 92 Data load time 25.9 sec nmask = 2680458, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 13, PadThresh 0.0001 Segmentations used for rescaling 174 Pons MEM: Size 422356 Peak: 955936 RSS: 283024 Data: 281264 Stk: 92 ___ 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.