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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