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
