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
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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Agrawal, Shubhi (NIH/NINDS) [E] -
Douglas Greve