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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