Hi Caspar,
My system is CentOS 6.5 64bit, gcc 4.47. I disable “Warning as Errors” on
Modules “ImageStatistics” , “Connectomics”, and “FiberTracking”.
I only remember mitkIntensityProfile.cpp Line 36 (ImagesStatistics Module)
caused –Wstrict-aliasing issue.
Wayne
On 14-04-29 2:23 AM, "Goch, Caspar Jonas" <[email protected]> wrote:
> Hi Wayne,
>
> if you have to disable the „Warnings as Errors“ we would like to know about
> it, as we currently strive to keep the main components of MITK warning-free if
> possible. Could you tell us your setup (OS version, compiler version) and
> which modules you had to disable it in? This would be handy to have as we do
> not have the resources to test all possible operating system/compiler
> combinations.
>
> Thank you,
> Caspar
>
>
> Von: Wayne Su [mailto:[email protected]]
> Gesendet: Montag, 28. April 2014 17:49
> An: Neher, Peter; [email protected]; Nolden, Marco
> Betreff: Re: [mitk-users] Save Fiber bundle
>
> Hi Peter,
>
> I pulled the latest code, enabled MITK_BUILD_ALL_PLUGIN option, and disable
> “Warnings as Errors” 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 “make” 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 what’s 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 “Ignoring unknown target “org_mitk_diffusionImaging” for
> installation”. 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 I’m 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 I’m trying is to load them into TrackVis. Because the
> dimension of the fiber bundle is no longer same as the one from DWI, they
> don’t align in TrackVis. I’m 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 (I’m 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 don’t match.
>
> Thanks,
> Wayne
>
>
>
>
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>
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