users > RE: Warp output unreadable in reformatx
Dec 29, 2017  01:12 PM | Dan Xie - UCSF
RE: Warp output unreadable in reformatx
Hi Torsten, 

I am for sure not running out of disk space, so I guess the registration step got crashed.  One trial that failed to proceed to warping gives this logged output:

hostname = ad8; short hostname = ad8
User path is /usr/local/sge/bin/linux-x64:/tmp/172508.1.long.q:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
Reference brain is refbrain/RFP_temp.nrrd
Reference brain stem is RFP
JOB ID =
Start time is: 1514577682 seconds
Root directory is /netapp/home/danustc/cmtkRegistration
Found brain name Jun13B2control (images/Jun13B2control.nrrd)
New working directory is: /netapp/home/danustc/cmtkRegistration, Old one was /netapp/home/danustc/cmtkRegistration
MYEXEC: CMD = mkdir -p Registration/affine/RFP_Jun13B2control_9dof.list exited with value 0
A: Running affine reg with command: /netapp/home/danustc/cmtk-build/bin/registration -i -v --dofs 6 --dofs 9 --dofs 6,12 --mi --accuracy 4 -o Registration/affine/RFP_Jun13B2control_9dof.list refbrain/RFP_temp.nrrd images/Jun13B2control.nrrd
INFO: number of threads set to 4 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.


Another example that has unreadable warp results has the following logged output:

[color=#0000ff]hostname = id60; short hostname = id60
User path is /usr/local/sge/bin/linux-x64:/tmp/172498.1.long.q:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
Reference brain is refbrain/RFP_temp.nrrd
Reference brain stem is RFP
JOB ID =
Start time is: 1514576542 seconds
Root directory is /netapp/home/danustc/cmtkRegistration
Found brain name Jun06A2GCDA (images/Jun06A2GCDA.nrrd)
New working directory is: /netapp/home/danustc/cmtkRegistration, Old one was /netapp/home/danustc/cmtkRegistration
MYEXEC: CMD = mkdir -p Registration/affine/RFP_Jun06A2GCDA_9dof.list exited with value 0
A: Running affine reg with command: /netapp/home/danustc/cmtk-build/bin/registration -i -v --dofs 6 --dofs 9 --dofs 6,12 --mi --accuracy 4 -o Registration/affine/RFP_Jun06A2GCDA_9dof.list refbrain/RFP_temp.nrrd images/Jun06A2GCDA.nrrd
INFO: number of threads set to 4 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
Entering resolution level 1 out of 5...
Entering resolution level 1 out of 5...
Entering resolution level 1 out of 5...
Entering resolution level 1 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 5 out of 5...
Entering resolution level 5 out of 5...
Entering resolution level 5 out of 5...
Entering resolution level 5 out of 5...
Resulting transformation parameters:
#0d: 5.990000
#1d: -27.700000
#2d: 86.000000
#3d: 1.782642
#4d: -1.175570
#5d: 0.000000
#6d: 1.021623
#7d: 1.291911
#8d: 0.771295
#9d: 0.000000
#10d: 0.009980
#11d: 0.003327
#12d: 143.812500
#13d: 106.642500
#14d: 59.500000
MYEXEC: CMD = /netapp/home/danustc/cmtk-build/bin/registration -i -v --dofs 6 --dofs 9 --dofs 6,12 --mi --accuracy 4 -o Registration/affine/RFP_Jun06A2GCDA_9dof.list refbrain/RFP_temp.nrrd images/Jun06A2GCDA.nrrd exited with value 0
inlist = Registration/affine/RFP_Jun06A2GCDA_9dof.list
W: outlist = Registration/warp/RFP_Jun06A2GCDA_warp_m0g160c8e1e-1x52r2.list
MYEXEC: CMD = mkdir -p "Registration/warp/RFP_Jun06A2GCDA_warp_m0g160c8e1e-1x52r2.list" exited with value 0
W: Running warp reg with command: /netapp/home/danustc/cmtk-build/bin/warp -v --registration-metric nmi --jacobian-weight 0.005 --fast -e 52 --grid-spacing 160 --energy-weight 1e-1 --refine 2 --coarsest 8 --ic-weight 0 --output-intermediate --mi --accuracy 8 -o Registration/warp/RFP_Jun06A2GCDA_warp_m0g160c8e1e-1x52r2.list Registration/affine/RFP_Jun06A2GCDA_9dof.list
INFO: number of threads set to 4 according to environment variable CMTK_NUM_THREADS
Reading input studylist Registration/affine/RFP_Jun06A2GCDA_9dof.list
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.[/color]



[color=#0000ff]I did not see any error message here, so I am very confused. [/color]

[color=#0000ff]Thanks for looking into my problems. Happy Holidays!
[/color]
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RE: Warp output unreadable in reformatx
Dec 29, 2017