jefferis
commented
6 years ago Thanks for your interest. I'm afraid that you are getting an exception in the underlying CMTK warp tool (search for Caught signal 11). Your best bet is to post a question on the CMTK user forum:
https://www.nitrc.org/forum/forum.php?forum_id=857 https://www.nitrc.org/forum/forum.php?forum_id=857
to get you started, I see the warp registration is failing part way through registration – when it gets to level 3. I do notice that you have a lot of parameters already at level 2:
Deactivated 286325976 out of 304966215 parameters.
most of which are being deactivated (because there is no information in that part of the image). I would suggest that there is a mismatch between the registration parameters and the spatial scale of your image and/or an initial misregistration. I would be surprised if you really want to use 1.5 billion params for level 3.
In fact on the topic of initial mis-registration the affine registration includes very large translations
12d: 90155.257586
13d: 90155.257586
14d: 49.500000
Is that 90000 microns in XY?
Best,
Greg.
On 8 Jun 2018, at 19:05, Mahmood-Hoseini notifications@github.com wrote:
Hello,
I'm using CMTK on an Ubuntu machine to affine, warp, and reformat my 2p images. It successfully affines and warps the images but fails to generate the reformatted images without any apparent error message (both terminal log and CMTK console are pasted here). I have tried this on a mac OS and still not able to generate the reformatted images. I appreciate your help.
-Mahmood
TERMINAL LOG `idl@mps-pc59:~/data/reg/commands$ sh munger_2018-06-07_10.05.31.sh hostname = mps-pc59; short hostname = mps-pc59 JOB ID = Root directory is /home/idl/data/reg Changing to root directory: /home/idl/data/reg Setting image root to: images MYEXEC: CMD = mkdir -p Registration/affine/Day0_Day10_01_9dof.list exited with value 0 Aff:Day10_01 INFO: number of threads set to 8 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 4... Entering resolution level 1 out of 4... Entering resolution level 2 out of 4... Entering resolution level 2 out of 4... Entering resolution level 3 out of 4... Entering resolution level 3 out of 4... Entering resolution level 4 out of 4... Entering resolution level 4 out of 4... Resulting transformation parameters:
0d: 0.000000
1d: 0.000000
2d: 0.000000
3d: 0.000000
4d: 0.000000
5d: 0.000000
6d: 1.000000
7d: 1.000000
8d: 1.000000
9d: 0.000000
10d: 0.000000
11d: 0.000000
12d: 90155.257586
13d: 90155.257586
14d: 49.500000
MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Day0_Day10_01_9dof.list refbrain/Day0_01.nrrd images/Day10_01.nrrd exited with value 0 MYEXEC: CMD = mkdir -p "Registration/warp/Day0_Day10_01_warpm0g80c8e1e-1x26r4.list" exited with value 0 Warp Day10,INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS Reading input studylist Registration/affine/Day0_Day10_01_9dof.list 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 4... Setting step size to 25.6 [mm] Deactivated 55108956 out of 61074432 parameters. Setting step size to 12.8 [mm] Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 2 out of 4... Setting step size to 12.8 [mm] Deactivated 286325976 out of 304966215 parameters. Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 3 out of 4... Caught signal 11, faulty address is (nil) [stack] Execution path: [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(cmtkStackBacktraceSignalHandler+0x23) [0x5bceea] [stack] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390) [0x7faf43398390] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk43VoxelMatchingElasticFunctional_WarpTemplateINS_15SplineWarpXformEE12SetWarpXformERNS_12SmartPointerIS1_EE+0x1a2) [0x4c7b82] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk39VoxelMatchingElasticFunctional_TemplateINS_23VoxelMatchingNormMutInfILNS_13Interpolators17InterpolationEnumE2EEEE12SetWarpXformERNS_12SmartPointerINS_15SplineWarpXformEEE+0x2a) [0x49ffc8] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk19ElasticRegistration15EnterResolutionERNS_12SmartPointerINS_6VectorIdEEEERNS1_INS_10FunctionalEEEii+0x128) [0x48929a] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk17VoxelRegistration8RegisterEv+0x6b2) [0x4cb34c] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk30ElasticRegistrationCommandLine8RegisterEv+0x1f) [0x4756ef] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_Z6doMainiPPKc+0xcd) [0x47544d] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(main+0x23) [0x472cde] [stack] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7faf4251a830] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(start+0x29) [0x4752a9] MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/warp -v --registration-metric nmi --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --output-intermediate --accuracy 0.4 -o Registration/warp/Day0_Day10_01_warp_m0g80c8e1e-1x26r4.list Registration/affine/Day0_Day10_01_9dof.list exited with value 1 Warp Day10,INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS Reading input studylist Registration/affine/Day0_Day10_01_9dof.list 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 4... Setting step size to 25.6 [mm] Deactivated 55108956 out of 61074432 parameters. Setting step size to 12.8 [mm] Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 2 out of 4... Setting step size to 12.8 [mm] Deactivated 286325976 out of 304966215 parameters. Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 3 out of 4... Caught signal 11, faulty address is (nil) [stack] Execution path: [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(cmtkStackBacktraceSignalHandler+0x23) [0x5bceea] [stack] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390) [0x7fa7632ad390] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk43VoxelMatchingElasticFunctional_WarpTemplateINS_15SplineWarpXformEE12SetWarpXformERNS_12SmartPointerIS1_EE+0x1a2) [0x4c7b82] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk39VoxelMatchingElasticFunctional_TemplateINS_23VoxelMatchingNormMutInfILNS_13Interpolators17InterpolationEnumE2EEEE12SetWarpXformERNS_12SmartPointerINS_15SplineWarpXformEEE+0x2a) [0x49ffc8] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk19ElasticRegistration15EnterResolutionERNS_12SmartPointerINS_6VectorIdEEEERNS1_INS_10FunctionalEEEii+0x128) [0x48929a] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk17VoxelRegistration8RegisterEv+0x6b2) [0x4cb34c] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk30ElasticRegistrationCommandLine8RegisterEv+0x1f) [0x4756ef] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_Z6doMainiPPKc+0xcd) [0x47544d] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(main+0x23) [0x472cde] [stack] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fa76242f830] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_start+0x29) [0x4752a9] MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/warp -v --registration-metric nmi --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --output-intermediate --accuracy 0.4 -o Registration/warp/Day0_Day10_01_warp_m0g80c8e1e-1x26r4.list Registration/affine/Day0_Day10_01_9dof.list exited with value 1
Ran 0 initial affine registrations of which 0 failed Ran 1 affine registrations of which 0 failed Ran 2 warp registrations Reformatted 0 images`
CMTK CONSOLE `bindir is /home/idl/bin/Fiji.app/bin/cmtk munger is /home/idl/bin/Fiji.app/bin/cmtk/munger Jefferis, Potter 2007 Chosen reg params: Cachero, Ostrovsky 2010 /home/idl/data/reg/refbrain//Day0_01.nrrd refbrain/Day0_01.nrrd Cachero, Ostrovsky 2010 "/home/idl/bin/Fiji.app/bin/cmtk/munger" -b "/home/idl/bin/Fiji.app/bin/cmtk" -a -w -r 01 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 8 -s "refbrain/Day0_01.nrrd" images script is /home/idl/data/reg/commands/munger_2018-06-07_10.05.31.sh [ERROR] null Traceback (most recent call last): File "CMTK_Registration/Help_For_CMTK_Tool.py", line 5, in NameError: name 'sys' is not defined
at org.python.core.Py.NameError(Py.java:284) at org.python.core.PyFrame.getname(PyFrame.java:257) at org.python.pycode._pyx4.f$0(CMTK_Registration/Help_For_CMTK_Tool.py:28) at org.python.pycode._pyx4.call_function(CMTK_Registration/Help_For_CMTK_Tool.py) at org.python.core.PyTableCode.call(PyTableCode.java:167) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.Py.runCode(Py.java:1386) at org.python.core.builtin.eval(builtin.java:497) at org.python.core.builtin.eval(builtin.java:501) at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259) at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:40) at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31) at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264) at org.scijava.script.ScriptModule.run(ScriptModule.java:160) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) `
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-- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics
Mahmood-Hoseini
Hello,
I'm using CMTK on an Ubuntu machine to affine, warp, and reformat my 2p images. It successfully affines and warps the images but fails to generate the reformatted images without any apparent error message (both terminal log and CMTK console are pasted here). I have tried this on a mac OS and still not able to generate the reformatted images. I appreciate your help.
-Mahmood
TERMINAL LOG `idl@mps-pc59:~/data/reg/commands$ sh munger_2018-06-07_10.05.31.sh hostname = mps-pc59; short hostname = mps-pc59 JOB ID = Root directory is /home/idl/data/reg Changing to root directory: /home/idl/data/reg Setting image root to: images MYEXEC: CMD = mkdir -p Registration/affine/Day0_Day10_01_9dof.list exited with value 0 Aff:Day10_01 INFO: number of threads set to 8 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 4... Entering resolution level 1 out of 4... Entering resolution level 2 out of 4... Entering resolution level 2 out of 4... Entering resolution level 3 out of 4... Entering resolution level 3 out of 4... Entering resolution level 4 out of 4... Entering resolution level 4 out of 4... Resulting transformation parameters:
0d: 0.000000
1d: 0.000000
2d: 0.000000
3d: 0.000000
4d: 0.000000
5d: 0.000000
6d: 1.000000
7d: 1.000000
8d: 1.000000
9d: 0.000000
10d: 0.000000
11d: 0.000000
12d: 90155.257586
13d: 90155.257586
14d: 49.500000
MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Day0_Day10_01_9dof.list refbrain/Day0_01.nrrd images/Day10_01.nrrd exited with value 0 MYEXEC: CMD = mkdir -p "Registration/warp/Day0_Day10_01_warpm0g80c8e1e-1x26r4.list" exited with value 0 Warp Day10,INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS Reading input studylist Registration/affine/Day0_Day10_01_9dof.list 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 4... Setting step size to 25.6 [mm] Deactivated 55108956 out of 61074432 parameters. Setting step size to 12.8 [mm] Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 2 out of 4... Setting step size to 12.8 [mm] Deactivated 286325976 out of 304966215 parameters. Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 3 out of 4... Caught signal 11, faulty address is (nil) [stack] Execution path: [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(cmtkStackBacktraceSignalHandler+0x23) [0x5bceea] [stack] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390) [0x7faf43398390] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk43VoxelMatchingElasticFunctional_WarpTemplateINS_15SplineWarpXformEE12SetWarpXformERNS_12SmartPointerIS1_EE+0x1a2) [0x4c7b82] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk39VoxelMatchingElasticFunctional_TemplateINS_23VoxelMatchingNormMutInfILNS_13Interpolators17InterpolationEnumE2EEEE12SetWarpXformERNS_12SmartPointerINS_15SplineWarpXformEEE+0x2a) [0x49ffc8] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk19ElasticRegistration15EnterResolutionERNS_12SmartPointerINS_6VectorIdEEEERNS1_INS_10FunctionalEEEii+0x128) [0x48929a] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk17VoxelRegistration8RegisterEv+0x6b2) [0x4cb34c] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk30ElasticRegistrationCommandLine8RegisterEv+0x1f) [0x4756ef] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_Z6doMainiPPKc+0xcd) [0x47544d] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(main+0x23) [0x472cde] [stack] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7faf4251a830] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_start+0x29) [0x4752a9] MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/warp -v --registration-metric nmi --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --output-intermediate --accuracy 0.4 -o Registration/warp/Day0_Day10_01_warp_m0g80c8e1e-1x26r4.list Registration/affine/Day0_Day10_019dof.list exited with value 1 Warp Day10,INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS Reading input studylist Registration/affine/Day0_Day10_01_9dof.list 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 4... Setting step size to 25.6 [mm] Deactivated 55108956 out of 61074432 parameters. Setting step size to 12.8 [mm] Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 2 out of 4... Setting step size to 12.8 [mm] Deactivated 286325976 out of 304966215 parameters. Setting step size to 6.4 [mm] Setting step size to 3.2 [mm] Setting step size to 1.6 [mm] Setting step size to 0.8 [mm] Setting step size to 0.4 [mm] Entering resolution level 3 out of 4... Caught signal 11, faulty address is (nil) [stack] Execution path: [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(cmtkStackBacktraceSignalHandler+0x23) [0x5bceea] [stack] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390) [0x7fa7632ad390] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk43VoxelMatchingElasticFunctional_WarpTemplateINS_15SplineWarpXformEE12SetWarpXformERNS_12SmartPointerIS1_EE+0x1a2) [0x4c7b82] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk39VoxelMatchingElasticFunctional_TemplateINS_23VoxelMatchingNormMutInfILNS_13Interpolators17InterpolationEnumE2EEEE12SetWarpXformERNS_12SmartPointerINS_15SplineWarpXformEEE+0x2a) [0x49ffc8] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk19ElasticRegistration15EnterResolutionERNS_12SmartPointerINS_6VectorIdEEEERNS1_INS_10FunctionalEEEii+0x128) [0x48929a] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk17VoxelRegistration8RegisterEv+0x6b2) [0x4cb34c] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_ZN4cmtk30ElasticRegistrationCommandLine8RegisterEv+0x1f) [0x4756ef] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_Z6doMainiPPKc+0xcd) [0x47544d] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(main+0x23) [0x472cde] [stack] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fa76242f830] [stack] /home/idl/bin/Fiji.app/bin/cmtk/warp(_start+0x29) [0x4752a9] MYEXEC: CMD = /home/idl/bin/Fiji.app/bin/cmtk/warp -v --registration-metric nmi --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --output-intermediate --accuracy 0.4 -o Registration/warp/Day0_Day10_01_warp_m0g80c8e1e-1x26r4.list Registration/affine/Day0_Day10_01_9dof.list exited with value 1
Ran 0 initial affine registrations of which 0 failed Ran 1 affine registrations of which 0 failed Ran 2 warp registrations Reformatted 0 images`
CMTK CONSOLE `bindir is /home/idl/bin/Fiji.app/bin/cmtk munger is /home/idl/bin/Fiji.app/bin/cmtk/munger Jefferis, Potter 2007 Chosen reg params: Cachero, Ostrovsky 2010 /home/idl/data/reg/refbrain//Day0_01.nrrd refbrain/Day0_01.nrrd Cachero, Ostrovsky 2010 "/home/idl/bin/Fiji.app/bin/cmtk/munger" -b "/home/idl/bin/Fiji.app/bin/cmtk" -a -w -r 01 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 8 -s "refbrain/Day0_01.nrrd" images script is /home/idl/data/reg/commands/munger_2018-06-07_10.05.31.sh [ERROR] null Traceback (most recent call last): File "CMTK_Registration/Help_For_CMTK_Tool.py", line 5, in
NameError: name 'sys' is not defined
`