Hi Peter,
I pulled the latest code, enabled MITK_BUILD_ALL_PLUGIN option, and disable
³Warnings as Errors² on some modules(if having compiling error). Now it
seems Diffusion GUI is working.
Thank you all of hard work.
Wayne
On 14-04-28 12:32 AM, "Peter Neher" <[email protected]> wrote:
> Hi Wayne,
>
> sorry for the late reply. Great that the MiniApps are working! As for your
> cmake warnings, you might try disabling the MITK_USE_Build_ALL_APPS option on
> the superbuild level and instead only enable everything that contains the word
> "diffusion" on the MITK build level (see attached screenshot).
>
> Marco, can you maybe comment on the cmake warnings?
>
> Best,
> Peter
>
>
> On 04/17/2014 06:21 PM, Wayne Su wrote:
>
>
>> Re: [mitk-users] Save Fiber bundle Hi Peter,
>>
>> I changed following configurations:
>> Build_Testing:ON --> OFF
>> CMake_Build_Type: Debug --> Release
>> MITK_USE_Boost: OFF --> ON
>> MITK_USE_SUPERBUILD: OFF--> ON
>> MITK_USE_Build_ALL_APPS: OFF--> ON
>>
>> The ³make² command was finished without error. MiniApps is working as I
>> expected (great work). When I run MitkDiffusion, I got following messages:
>>
>> *0.970* [BlueBerry] FATAL: No extensions configured into extension-point
>> 'org.blueberry.osgi.applications' found. Aborting.
>> #0.970# [BlueBerry] ERROR: Could not create executable application extension
>> for id: org.mitk.qt.diffusionimagingapp
>>
>> I checked the build process, and found following warnings:
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_coreapplication" for
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/CoreApp/CMakeLists.txt:26
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_diffusionimaging" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_diffusionimagingapp" for
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_common_legacy" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_measurementtoolbox" for
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_segmentation" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_volumevisualization" for
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_diffusionimaging" for
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_moviemaker" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_basicimageprocessing" for "
>> installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_registration" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_gui_qt_common_legacy" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> CMake Warning at CMake/mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>> Ignoring unknown target "org_mitk_diffusionimaging" for installation.
>> Call Stack (most recent call first):
>> CMake/mitkFunctionInstallAutoLoadModules.cmake:102
>> (mitkFunctionInstallAutoLoadModules)
>> BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake:208
>> (BlueBerryApplicationInstallHook)
>> Applications/Diffusion/CMakeLists.txt:63
>> (FunctionCreateBlueBerryApplication)
>>
>>
>> Do you think what¹s wrong with it?
>>
>> Thanks,
>> Wayne
>>
>>
>> On 14-04-17 1:50 AM, "Peter Neher" <[email protected]> wrote:
>>
>>
>>> Are you trying to build an installer? What did you enable in cmake?
>>>
>>>
>>> On 04/16/2014 06:48 PM, Wayne Su wrote:
>>>
>>>
>>>
>>>> Re: [mitk-users] Save Fiber bundle Hi Peter,
>>>> Thank you for delivering the good news. I tried to compile new release
>>>> of MITK from the source code in order to get MitkDiffusion and MiniApps.
>>>> And I got some errors ³Ignoring unknown target ³org_mitk_diffusionImaging²
>>>> for installation². I guess I have to wait the formal release of
>>>> MitkDiffusion.
>>>>
>>>> Wayne
>>>>
>>>>
>>>> On 14-04-16 6:13 AM, "Peter Neher" <[email protected]> wrote:
>>>>
>>>>
>>>>
>>>>> Hi Wayne,
>>>>>
>>>>> I think the new release of MITK will support the trackvis file format,
>>>>> at least if you perform the tracking using the MiniApp command line tool.
>>>>> But to include the geometry of the image in the output file will only
>>>>> work for the miniApp, not the GUI application. In the miniApp it is
>>>>> possible to directly associate the image with the tractogram, which is in
>>>>> general not possible in the GUI. The new release of MitkDiffusion will be
>>>>> available soon and hopefully also the MiniApps.
>>>>>
>>>>> Cheers,
>>>>> Peter
>>>>>
>>>>>
>>>>> On 04/11/2014 10:19 PM, Wayne Su wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Re: Save Fiber bundle TrackVis uses LPS coordinate system. But the
>>>>>> fiber bundle saved by MITK uses RAS coordinate system. I managed to edit
>>>>>> the dimension of track file, and translate x and y values in the track
>>>>>> file. Finally I got aligned track and DWI in TrackVis program.
>>>>>>
>>>>>> If I¹m correct, I suggest to save TrackVis track file in LAS instead
>>>>>> RAS coordinate system. And use the full dimension of upsampled DWI in
>>>>>> 1x1x1 resolution, or maybe native DWI space. All this needs to modify
>>>>>> MITK source code.
>>>>>>
>>>>>> Wayne
>>>>>>
>>>>>>
>>>>>> On 14-04-11 8:50 AM, "Wayne Su" <[email protected]> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Christian,
>>>>>>>
>>>>>>> Thank you for the reply. In the MITK-DT, the fiber bundle aligns well
>>>>>>> with T1 and DWI. What I¹m trying is to load them into TrackVis. Because
>>>>>>> the dimension of the fiber bundle is no longer same as the one from DWI,
>>>>>>> they don¹t align in TrackVis. I¹m wondering whether there is any option
>>>>>>> to use the dimension of DWI (maybe the upsampled DWI with 1x1x1
>>>>>>> resolution) to save fiber bundle. I know there are two ways. One
>>>>>>> solution is to crop DWI to match fiber bundle. Another way is to change
>>>>>>> the dimension of fiber bundle (I¹m not familiar with this part). I
>>>>>>> appreciate any input on this case.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Wayne
>>>>>>>
>>>>>>>
>>>>>>> On 14-04-11 12:56 AM, "Weber, Christian(1)"
>>>>>>> <[email protected]> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
Hi Wyane,
the fiber bundles are allways in the space of DWI since they are derived
from it.
Since DWI and T1/T2 often do not match you need to register them,
currently the easiest way doing this with GUI is
(AFAIK ):
Extract B0 image from the DWI and then register the T1 to this B0 image,
using e.g. the Point-Based registration.
Best,
Christian
From: Wayne Su [mailto:[email protected]]
Sent: Donnerstag, 10. April 2014 20:10
To: [email protected]
Subject: [mitk-users] Save Fiber bundle
Hello experts,
Is there a way to save diffusion fiber bundle onto T1 structural space or
DWI space, i.e. the dimension of the fiber bundle is the same as the one
from T1 or DWI? Currently, it saves as reduced dimension with 1mmx1mmx1mm
spacing. I tried to load the track file into TrackVis along with T1 image.
But the locations of them don¹t match.
Thanks,
Wayne
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>
>
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