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(23680000,100): 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 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta Data load time 24.9 sec nmask = 23680000, 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-request@nmr.mgh.harvard.edu [freesurfer-request@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-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@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 (miracooloz@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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Petsurfer mri_gtmpvc error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 7422f5df-b0e5-587b-d71c-7dd2cc14aba3@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 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 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