Did you really mean to pass subject/mri/gtmseg.lta ? The registration is
supposed to be the registration of the input (PET.template.nii.gz) to
the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz
to the anatomical.
On 7/20/20 11:21 AM, Crawford, Anna wrote:
External Email - Use Caution
Hello,
I am trying to run the PetSurfer process for the first time. I was
able to run gtmseg and mri_coreg which seemed to go okay. When I tried
running mri_gtmpvc, it is crashing, but I am not sure why. The command
I am using and output are below. Do you have any guidance as to what
is going wrong?
Thank you,
Anna
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o
subject/gtmpvc.output
Loading input ../CTPET/PET.template.nii.gz
done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o
subject/gtmpvc.output
sysname Linux
hostname fmri15
machine x86_64
user crawforda
vgthresh 0.001000
nReplace 18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3 235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 -------------------
type = 0 # LINEAR_VOX_TO_VOX
nxforms = 1
mean = 0.0000 0.0000 0.0000
sigma = 10000.0000
1 4 4
9.999997615814209e-01 0.000000000000000e+00 -8.381903171539307e-09
-7.629394531250000e-06
7.450580596923828e-09 9.999998807907104e-01 0.000000000000000e+00
0.000000000000000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.999998211860657e-01
-1.525878906250000e-05
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
9.999999403953552e-01
src volume info
valid = 1 # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000000000000000e+00 1.000000000000000e+00
1.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00
yras = 0.000000000000000e+00 0.000000000000000e+00
-1.000000000000000e+00
zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
cras = 4.125000000000000e+00 3.554792785644531e+01
-2.000000000000000e+01
dst volume info
valid = 1 # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000000000000000e+00 1.000000000000000e+00
1.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00
yras = 0.000000000000000e+00 0.000000000000000e+00
-1.000000000000000e+00
zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
cras = 4.125000000000000e+00 3.554792785644531e+01
-2.000000000000000e+01
subject subject
fscale 0.150000
LTA 1 -------------------
type = 0 # LINEAR_VOX_TO_VOX
nxforms = 1
mean = 0.0000 0.0000 0.0000
sigma = 10000.0000
1 4 4
9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
-2.099999237060547e+01
0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
-1.100000762939453e+01
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
-3.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00
src volume info
valid = 1 # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00
2.029999971389771e+00
xras = -1.000000000000000e+00 -0.000000000000000e+00
0.000000000000000e+00
yras = -0.000000000000000e+00 1.000000000000000e+00
0.000000000000000e+00
zras = -0.000000000000000e+00 -0.000000000000000e+00
1.000000000000000e+00
cras = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1 # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00
2.029999971389771e+00
xras = -1.000000000000000e+00 -0.000000000000000e+00
0.000000000000000e+00
yras = -0.000000000000000e+00 1.000000000000000e+00
0.000000000000000e+00
zras = -0.000000000000000e+00 -0.000000000000000e+00
1.000000000000000e+00
cras = -1.861288452148438e+01 1.840597229003906e+02
1.250690063476562e+03
--------------------------
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding segid=0
FWHM: 6 6 6
Std: 2.54797 2.54797 2.54797
nPad 10, PadThresh 0.0001
Checking Ref Ids
Segmentations used for rescaling
174 Pons
Computing Seg PVF
Segmentation fault (core dumped)
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