Hello, I am currently trying to run the install_CMTK.py through fiji and I keep getting the following error:

Started Install_CMTK.py at Thu Mar 12 11:31:16 EDT 2020
Traceback (most recent call last):
File "C:\Users\danah\OneDrive\Desktop\Fiji.dir\plugins\CMTK_Registration\CMTK\Install_CMTK.py", line 11, in
import cmtkgui
File "__pyclasspath__/cmtkgui$py.class", line 5, in
File "C:\Users\danah\OneDrive\Desktop\Fiji.dir\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 799, in
File "C:\Users\danah\OneDrive\Desktop\Fiji.dir\jars\jython-shaded-2.7.1.jar\Lib\subprocess.py", line 1399, in Popen
File "C:\Users\danah\OneDrive\Desktop\Fiji.dir\jars\jython-shaded-2.7.1.jar\Lib\ctypes\__init__.py", line 281, in __getattr__
File "C:\Users\danah\OneDrive\Desktop\Fiji.dir\jars\jython-shaded-2.7.1.jar\Lib\ctypes\__init__.py", line 262, in __init__
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.newLoadError(Foreign.java:72)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.access$300(Foreign.java:42)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InValidInstanceHolder.getForeign(Foreign.java:98)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103)
at org.scijava.jython.shaded.com.kenai.jffi.Library.openLibrary(Library.java:157)
at org.scijava.jython.shaded.com.kenai.jffi.Library.getCachedInstance(Library.java:131)
at org.python.modules.jffi.DynamicLibrary.(DynamicLibrary.java:26)
at org.python.modules.jffi.jffi.dlopen(jffi.java:43)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
java.lang.UnsatisfiedLinkError: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I

at org.python.core.Py.JavaError(Py.java:552)
at org.python.core.Py.JavaError(Py.java:543)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:206)
at org.python.core.PyObject.__call__(PyObject.java:497)
at org.python.core.PyObject.__call__(PyObject.java:501)
at ctypes$py.__init__$49(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py:262)
at ctypes$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.PyBaseCode.call(PyBaseCode.java:199)
at org.python.core.PyFunction.__call__(PyFunction.java:482)
at org.python.core.PyFunction.__call__(PyFunction.java:476)
at org.python.core.PyInstance.__init__(PyInstance.java:124)
at org.python.core.PyClass.__call__(PyClass.java:193)
at org.python.core.PyObject.__call__(PyObject.java:480)
at org.python.core.PyObject.__call__(PyObject.java:484)
at ctypes$py.__getattr__$54(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py:283)
at ctypes$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/ctypes/__init__.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:154)
at org.python.core.PyFunction.__call__(PyFunction.java:423)
at org.python.core.PyMethod.__call__(PyMethod.java:141)
at org.python.core.PyMethod.__call__(PyMethod.java:132)
at org.python.core.Deriveds.__findattr_ex__(Deriveds.java:81)
at org.python.core.PyObjectDerived.__findattr_ex__(PyObjectDerived.java:1036)
at org.python.core.PyObject.__getattr__(PyObject.java:1025)
at subprocess$py.Popen$22(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:1886)
at subprocess$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.Py.makeClass(Py.java:2066)
at org.python.core.Py.makeClass(Py.java:2060)
at subprocess$py.f$0(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py:2013)
at subprocess$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/subprocess.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.imp.createFromCode(imp.java:436)
at org.python.core.util.importer.importer_load_module(importer.java:116)
at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170)
at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.__call__(Unknown Source)
at org.python.core.PyBuiltinMethodNarrow.__call__(PyBuiltinMethodNarrow.java:46)
at org.python.core.imp.loadFromLoader(imp.java:593)
at org.python.core.imp.find_module(imp.java:547)
at org.python.core.imp.import_next(imp.java:838)
at org.python.core.imp.import_module_level(imp.java:957)
at org.python.core.imp.importName(imp.java:1057)
at org.python.core.ImportFunction.__call__(__builtin__.java:1280)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1076)
at cmtkgui$py.f$0(C:/Users/danah/OneDrive/Desktop/Fiji.app/plugins/CMTK_Registration/cmtkgui.py:372)
at cmtkgui$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.app/plugins/CMTK_Registration/cmtkgui.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.imp.createFromCode(imp.java:436)
at org.python.core.util.importer.importer_load_module(importer.java:116)
at org.python.core.ClasspathPyImporter.ClasspathPyImporter_load_module(ClasspathPyImporter.java:170)
at org.python.core.ClasspathPyImporter$ClasspathPyImporter_load_module_exposer.__call__(Unknown Source)
at org.python.core.PyBuiltinMethodNarrow.__call__(PyBuiltinMethodNarrow.java:46)
at org.python.core.imp.loadFromLoader(imp.java:593)
at org.python.core.imp.find_module(imp.java:547)
at org.python.core.imp.import_next(imp.java:838)
at org.python.core.imp.import_module_level(imp.java:957)
at org.python.core.imp.importName(imp.java:1057)
at org.python.core.ImportFunction.__call__(__builtin__.java:1280)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1076)
at org.python.pycode._pyx24.f$0(C:/Users/danah/OneDrive/Desktop/Fiji.dir/plugins/CMTK_Registration/CMTK/Install_CMTK.py:81)
at org.python.pycode._pyx24.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/plugins/CMTK_Registration/CMTK/Install_CMTK.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.newLoadError(Foreign.java:72)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.access$300(Foreign.java:42)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InValidInstanceHolder.getForeign(Foreign.java:98)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103)
at org.scijava.jython.shaded.com.kenai.jffi.Library.openLibrary(Library.java:157)
at org.scijava.jython.shaded.com.kenai.jffi.Library.getCachedInstance(Library.java:131)
at org.python.modules.jffi.DynamicLibrary.(DynamicLibrary.java:26)
at org.python.modules.jffi.jffi.dlopen(jffi.java:43)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:188)
... 86 more
Caused by: java.lang.UnsatisfiedLinkError: org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion()I
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getVersion(Native Method)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InstanceHolder.getInstanceHolder(Foreign.java:53)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign$InstanceHolder.(Foreign.java:45)
at org.scijava.jython.shaded.com.kenai.jffi.Foreign.getInstance(Foreign.java:103)
at org.scijava.jython.shaded.com.kenai.jffi.Type$Builtin.lookupTypeInfo(Type.java:242)
at org.scijava.jython.shaded.com.kenai.jffi.Type$Builtin.getTypeInfo(Type.java:237)
at org.scijava.jython.shaded.com.kenai.jffi.Type.resolveSize(Type.java:155)
at org.scijava.jython.shaded.com.kenai.jffi.Type.size(Type.java:138)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime$TypeDelegate.size(NativeRuntime.java:187)
at org.scijava.jython.shaded.jnr.ffi.provider.AbstractRuntime.(AbstractRuntime.java:48)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.(NativeRuntime.java:66)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.(NativeRuntime.java:41)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime$SingletonHolder.(NativeRuntime.java:62)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.NativeRuntime.getInstance(NativeRuntime.java:58)
at org.scijava.jython.shaded.jnr.ffi.provider.jffi.Provider.(Provider.java:29)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider$SystemProviderSingletonHolder.getInstance(FFIProvider.java:68)
at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider$SystemProviderSingletonHolder.(FFIProvider.java:57)
at org.scijava.jython.shaded.jnr.ffi.provider.FFIProvider.getSystemProvider(FFIProvider.java:35)
at org.scijava.jython.shaded.jnr.ffi.Library.loadLibrary(Library.java:114)
at org.scijava.jython.shaded.jnr.posix.POSIXFactory$DefaultLibCProvider$SingletonHolder.(POSIXFactory.java:279)
at org.scijava.jython.shaded.jnr.posix.POSIXFactory$DefaultLibCProvider.getLibC(POSIXFactory.java:283)
at org.scijava.jython.shaded.jnr.posix.BaseNativePOSIX.(BaseNativePOSIX.java:37)
at org.scijava.jython.shaded.jnr.posix.WindowsPOSIX.(WindowsPOSIX.java:132)
at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadWindowsPOSIX(POSIXFactory.java:163)
at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadNativePOSIX(POSIXFactory.java:136)
at org.scijava.jython.shaded.jnr.posix.POSIXFactory.loadPOSIX(POSIXFactory.java:90)
at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.loadPOSIX(LazyPOSIX.java:38)
at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.posix(LazyPOSIX.java:32)
at org.scijava.jython.shaded.jnr.posix.LazyPOSIX.isNative(LazyPOSIX.java:382)
at org.python.modules.posix.PosixModule.classDictInit(PosixModule.java:131)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.PyJavaType.init(PyJavaType.java:571)
at org.python.core.PyType.createType(PyType.java:1523)
at org.python.core.PyType.addFromClass(PyType.java:1462)
at org.python.core.PyType.fromClass(PyType.java:1551)
at org.python.core.imp.createFromClass(imp.java:469)
at org.python.core.imp.loadBuiltin(imp.java:578)
at org.python.core.imp.find_module(imp.java:534)
at org.python.core.imp.import_next(imp.java:838)
at org.python.core.imp.import_module_level(imp.java:957)
at org.python.core.imp.importName(imp.java:1057)
at org.python.core.ImportFunction.__call__(__builtin__.java:1280)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importAll(imp.java:1176)
at os$py.f$0(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/os.py:726)
at os$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/os.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.imp.createFromCode(imp.java:436)
at org.python.core.util.importer.importer_load_module(importer.java:116)
at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170)
at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.__call__(Unknown Source)
at org.python.core.PyBuiltinMethodNarrow.__call__(PyBuiltinMethodNarrow.java:46)
at org.python.core.imp.loadFromLoader(imp.java:593)
at org.python.core.imp.find_module(imp.java:547)
at org.python.core.imp.import_next(imp.java:838)
at org.python.core.imp.import_module_level(imp.java:957)
at org.python.core.imp.importName(imp.java:1057)
at org.python.core.ImportFunction.__call__(__builtin__.java:1280)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1076)
at site$py.f$0(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/site.py:637)
at site$py.call_function(C:/Users/danah/OneDrive/Desktop/Fiji.dir/jars/jython-shaded-2.7.1.jar/Lib/site.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.imp.createFromCode(imp.java:436)
at org.python.core.util.importer.importer_load_module(importer.java:116)
at org.python.modules.zipimport.zipimporter.zipimporter_load_module(zipimporter.java:170)
at org.python.modules.zipimport.zipimporter$zipimporter_load_module_exposer.__call__(Unknown Source)
at org.python.core.PyBuiltinMethodNarrow.__call__(PyBuiltinMethodNarrow.java:46)
at org.python.core.imp.loadFromLoader(imp.java:593)
at org.python.core.imp.find_module(imp.java:547)
at org.python.core.imp.import_next(imp.java:838)
at org.python.core.imp.import_first(imp.java:863)
at org.python.core.imp.load(imp.java:721)
at org.python.core.Py.importSiteIfSelected(Py.java:1795)
at org.python.util.PythonInterpreter.(PythonInterpreter.java:116)
at org.python.util.PythonInterpreter.threadLocalStateInterpreter(PythonInterpreter.java:81)
at org.python.jsr223.PyScriptEngine.(PyScriptEngine.java:27)
at org.python.jsr223.PyScriptEngineFactory.getScriptEngine(PyScriptEngineFactory.java:85)
at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:140)
at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:108)
at org.scijava.script.ScriptModule.run(ScriptModule.java:129)
... 8 more


The error the program keeps throwing is an unsatisfied link error in the pathway for java.lang.systems in the code. I am very naive to coding (particularly python-based languages) so I can't seem to figure out how to satisfy the error. I appreciate any and all help!

Hello Dana,

I'm afraid that the Windows installation has generally been unreliable. Right now the best thing that I can suggest is

1. Install the CMTK software directly from nitrc (I recommend the cygwin versions rather than the pure windows versions)

You can see some tips here http://natverse.org/nat/articles/Installation.html#cmtknat-on-windows

2. Use the Fiji CMTK GUI to generate shell scripts 

3. You can than edit the scripts to replace the location of the munger script and CMTK binaries

"/Applications/Fiji.app/bin/cmtk/munger"

"/Applications/Fiji.app/bin/cmtk"

with their installed locations

in the terminal to find them.

Best,

Greg.

Hi Dana,

    I'm not sure what you plan to use CMTK for, but I've had some success installing CMTK on my Windows machine. I'm using CMTK to register images of Drosophila brains. I've attached the instructions I wrote here, on the off chance that you find them helpful. They were modified from those found at researchmap.jp/t_m/.

~Gabriella

Hi Dana, 

I am also using CMTK on windows, but I am using WSL https://docs.microsoft.com/en-us/windows/wsl/about. I think that might be easier than trying to use Cygwin as Greg suggested. At least it was easier for me. With WSL you can just install the linux version of CMTK. I followed these instructions:
https://www.nitrc.org/forum/forum.php?th...
making sure to enable to optional tools during ccmake to install munger
https://www.nitrc.org/forum/message.php?...

You wont have the GUI this way, but once you have a munger script that runs it is very easy to modify it to run whatever new data you want to register.

Dear Gabriella and Owen,

Many thanks for your helpful suggestions.

Owen as you can see, I have not used wsl but this certainly sounds like an interesting option. Does it come with its own terminal, path etc? Where does cmtk normally get installed on such a system?

Dana, the only advantage of the cygwin approach may be that the binaries are likely to work fine, whereas we have run into issues with the linux binaries on different versions of linux. As you will see, Owen compiled CMTK source (this is not hard following the instructions, but there are a few steps to take).

Best,

Greg.

Originally posted by Owen Randlett:

It gives you a terminal. you can install whatever version of linux you want I think. I just installed Ubuntu from the Microsoft App store. You can also access the path of the linux directory from windows and vice versa, but I guess this is not recommended. 

You get a home directory, and can chose where to install programs like normal.

Combining it with VS Code running in Windows is working quite nicely for me - https://code.visualstudio.com/docs/remote/wsl

Hi Dr. Jefferis,

I appreciate your help! I am going to first attempt Dr. Randlett's method using WSL and VScode. But I still appreciate the insight. Thank you again.

Originally posted by Owen Randlett: Hi Dr. Randlett,

Thank you for your help! I am going to attempt your method using WSL since my use of CMTK is for your pERK MAP-mapping technique. Hopefully all goes well!

Best,
Dana