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
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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
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