External Email - Use Caution
My mistake, I think that fixed it.
Thank you!
Anna
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<dgr...@mgh.harvard.edu>
Sent: Monday, July 20, 2020 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] PetSurfer Crashing
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<http://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)
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation's top hospitals by
U.S. News & World Report (2019-2020). Visit us online at
http://www.clevelandclinic.org<http://www.clevelandclinic.org> for a complete
listing of our services, staff and locations. Confidentiality Note: This
message is intended for use only by the individual or entity to which it is
addressed and may contain information that is privileged, confidential, and
exempt from disclosure under applicable law. If the reader of this message is
not the intended recipient or the employee or agent responsible for delivering
the message to the intended recipient, you are hereby notified that any
dissemination, distribution or copying of this communication is strictly
prohibited. If you have received this communication in error, please contact
the sender immediately and destroy the material in its entirety, whether
electronic or hard copy. Thank you.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by
U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services, staff
and locations. Confidentiality Note: This message is intended for use only by
the individual or entity to which it is addressed and may contain information
that is privileged, confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended recipient or the
employee or agent responsible for delivering the message to the intended
recipient, you are hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If you have received this
communication in error, please contact the sender immediately and destroy the
material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
