Hi Sascha,
I appreciate your help a lot.
Eventually, I managed with the building process and got a DiffusionImaging
module.
Actually, the problem was the timing of the building process (the conning),
I should have checked the dashboard!
Anyway, now I can work with that, it seems like a very helpful tool to my
research.
Thank you again!
Best Regards,
Miri
On Wed, Feb 8, 2012 at 1:40 PM, Sascha Zelzer
<[email protected]>wrote:
> Hi Miri,
>
> your settings look okay, but it is very difficult to diagnose such
> problems via email.
>
> If you just want to get started with diffusion imaging, you could set the
> BOOST_ROOT variable manually to your own Boost sources (you do not need to
> touch MITK_USE_Boost_LIBRARIES):
>
> 1.) Download Boost here
> http://mitk.org/download/thirdparty/boost_1_45_0.tar.bz2 and extract it
> to C:\
> 2.) Open CMake GUI and choose C(?):/MITK-superbuild/ as build directory
> 3.) Set the BOOST_ROOT variable to C:/boost_1_45_0 (add the variable with
> "Add Entry" if it does not show up
> 4.) Set MITK_USE_Boost to ON
> 5.) Build the C(?):/MITK-superbuild/MITK-supberbuild.sln solution
>
> Best,
> Sascha
>
>
> On 02/07/2012 08:47 PM, Miri Trope wrote:
>
> Hi Sascha,
>
> I did those and still got some errors like this (each one of them
> regarding the same problem of Boost):
>
> ---------------------------------------------------------------
> CMake Error at C:/Program Files/CMake
> 2.8/share/cmake-2.8/Modules/FindBoost.cmake:1135 (message):
> Unable to find the requested Boost libraries.
> Unable to find the Boost header files. Please set BOOST_ROOT to the root
> directory containing Boost or BOOST_INCLUDEDIR to the directory containing
> Boost's headers.
>
> CMake Error: The following variables are used in this project, but they
> are set to NOTFOUND.
>
> Please set them or make sure they are set and tested correctly in the
> CMake files:
>
> Boost_INCLUDE_DIR (ADVANCED)
>
> used as include directory in directory
> D:/MITK-root/MITK/Modules/DiffusionImaging
>
> used as include directory in directory
> D:/MITK-root/MITK/Modules/DiffusionImaging/Testing
>
> used as include directory in directory
> D:/MITK-root/MITK/Modules/Bundles/org.mitk.diffusionimaging
>
> used as include directory in directory
> D:/MITK-root/MITK/Modules/Bundles/org.mitk.gui.qt.diffusionimaging
>
> ---------------------------------------------------------
>
> Here is what I did exactly:
> =====================
>
> 1. in cmake toggle on:
> - MITK_USE_Boost, MITK_USE_Boost_LIBRARIES etc ...
>
> 2. after the build process rebuild separately Boost
>
> 3. in cmake change the build directory to: A/MITK-superbuild/MITK-build
> and toggle on:
> - org.mitk.gui.qt.diffusionimagingapp,
> org.mitk.gui.qt.diffusionimaging, org.mitk.diffusionimaging,
> MITK_USE_Boost_LIBRARIES etc...
>
> 4. those errors return from the configuration process in cmake
>
> What have I missed?
> Best,
> Miri
>
>
> On Tue, Feb 7, 2012 at 2:23 PM, Sascha Zelzer <[email protected]
> > wrote:
>
>> Hi Miri,
>>
>> Thanks for the buildlog. Are you sure you enabled the MITK_USE_Boost
>> option in the CMake GUI? The build directory in the GUI should point to:
>>
>> C:/MITK-root/MITK-superbuild
>>
>>
>> If you are still getting the same error, you can try to open the
>>
>> C:/MITK-root/MITK-superbuild/MITK-superbuild.sln
>>
>> Visual Studio solution and right-click on the "Boost" project and click
>> on "Rebuild".
>>
>> Hope this helps,
>>
>> Sascha
>>
>>
>> On 02/07/2012 10:45 AM, Miri Trope wrote:
>>
>> Hi Iggy,
>>
>> Thank you for your helpful information, you've motivated me to use
>> diffusionImaging :-)
>> I'm trying to build again MITK with BOOST toggle on, but I'm dealing with
>> some building errors:
>>
>> CMake Error at C:/Program Files (x86)/CMake
>> 2.8/share/cmake-2.8/Modules/FindBoost.cmake:1135 (message):
>> 10> Unable to find the requested Boost libraries.
>> 10> Unable to find the Boost header files. Please set BOOST_ROOT to the
>> root
>> 10> directory containing Boost or BOOST_INCLUDEDIR to the directory
>> containing
>> 10> Boost's headers.
>>
>> I guess that the building process hasn't download the whole Boost
>> package, because A/CMakeExternals/Install/BOOST/
>> lib/boost-1.X is missing. But I read
>> here<http://docs.mitk.org/nightly-qt4/BuildInstructionsPage.html>that it
>> should download boost 1.45.0 automatically.
>>
>> Attached BuildLog.
>> What do you think that is missing?
>>
>> Regards,
>> Miri
>>
>> On Mon, Feb 6, 2012 at 11:02 AM, Reicht, Ignaz <
>> [email protected]> wrote:
>>
>>> Hi Miri,
>>>
>>> so far you have to activate the diffusionimaging module
>>> (org.mitk.diffusionimaging). this module has its own factory which calls
>>> appropriate mechanisms for fiber visualization (3D and 2D). the
>>> mitkDiffusionimagefactory initializes the fiberbundlexmappers which are
>>> responsible for rendering. if you want to interact with and process on your
>>> fibers (colorcodings, cutting, etc.) org.mitk.gui.qt.diffusionimaging
>>> provides efficient tools / views to do so.
>>>
>>> org.mitk.gui.qt.diffusionimagingapp
>>> this is the bundle used for the standalone app for diffusionimaging (see
>>> http://www.mitk.org/wiki/DiffusionImaging)
>>>
>>> The diffusionimaging module requires some headers of the Boost library,
>>> therefore toggle this option (if not automatically done by CMake) and the
>>> superbuild mechanism will take care of downloading all required Boost data.
>>>
>>> For your own application, if you dont want to use the diffusionimaging
>>> module, mitkFiberBundleX, mitkFiberBundleXMapper2D/3D need to be ported to
>>> your directory/module hosting all datastructures of your task.
>>>
>>> iggy
>>>
>>> -------------------------------------------------
>>> Spelling Errors added by Apple OSX
>>> intelligent word completion
>>>
>>> On Feb 5, 2012, at 10:53 PM, Miri Trope wrote:
>>>
>>> Dear Peter,
>>>
>>> Your suggestions were very helpful and I managed with this stage by
>>> fstream ...
>>> But, in order to use mitkFiberBundleX:
>>>
>>> - all the components of mitkDiffusionImaging must be built by CMake in
>>> the configuration process?
>>> |____org.mitk.diffusionimaging
>>> |____org.mitk.gui.qt.diffusionimaging
>>> |____org.mitk.gui.qt.diffusionimagingapp
>>>
>>> - I've tried to build those, but the MITK_use_Boost is needed- a stage
>>> that I haven't succeeded to manage with due to some build errors ...
>>>
>>> There is other way to use this filter without the need of its building
>>> process?
>>>
>>>
>>> On Thu, Feb 2, 2012 at 2:55 PM, Peter Neher <[email protected]
>>> <mailto:[email protected]>> wrote:
>>> Hi Miri,
>>>
>>> .mat file import in MITK is not supported. You would either need to
>>> export your matlab datastructure as vtk file format (maybe this site can
>>> help you with that: http://www.exolete.com/recipes/matlab_vtk) or you'd
>>> have to find some other way to import your data into mitk. If its just a
>>> list of points it should not be too difficult to read the file using
>>> fstream.
>>>
>>> Peter
>>>
>>>
>>> On 02.02.2012 13:43, Miri Trope wrote:
>>> Dear Peter,
>>>
>>>
>>> Thank you very much for your kind and detailed explanation.
>>> Please forgive me about the following q:
>>> my fiber's data (fibers.mat) is represented as a structural object in
>>> Matlab.
>>> Does Mitk enable to import such a Matlab's data?
>>> Anyway, how my program can read the data from that fiber.mat file?
>>>
>>>
>>> Thanks in advance.
>>>
>>>
>>> On Thu, Feb 2, 2012 at 1:00 PM, Peter Neher <[email protected]
>>> <mailto:[email protected]>> wrote:
>>> Hi Miri,
>>>
>>> to represent fiber tracts we use mitkFiberBundleX. This datastructure is
>>> simply initialized using a vtkPolyData containing all your fiber data.
>>> Simple example:
>>>
>>> vtkSmartPointer<vtkPolyData> fiberPolyData =
>>> vtkSmartPointer<vtkPolyData>::New(); // the input datastructure for
>>> mitkFiberBundleX
>>> vtkSmartPointer<vtkCellArray> fiberContainer =
>>> vtkSmartPointer<vtkCellArray>::New();
>>> vtkSmartPointer<vtkPoints> pointContainer =
>>> vtkSmartPointer<vtkPoints>::New();
>>>
>>> for (int l=0; l<numlines; l++) // iterate over fibers
>>> {
>>> vtkSmartPointer<vtkPolyLine> fiber =
>>> vtkSmartPointer<vtkPolyLine>::New();
>>> for (int p=0; p<pointsInLine; p++) // iterate over points in fiber
>>> {
>>> vtkIdType id = pointContainer->InsertNextPoint(yourPoint); //
>>> add next point
>>> fiber->GetPointIds()->InsertNextId(id); // add point id to
>>> fiber
>>> }
>>> fiberContainer->InsertNextCell(fiber); // add fiber to fiber
>>> container
>>> }
>>>
>>> fiberPolyData->SetPoints(pointContainer);
>>> fiberPolyData->SetLines(fiberContainer);
>>>
>>> mitk::FiberBundleX::Pointer fiberBundle =
>>> mitk::FiberBundleX::New(fiberPolyData);
>>>
>>> Peter
>>>
>>>
>>> On 02.02.2012 07:47, Miri Trope wrote:
>>> Hi All,
>>>
>>> How I should convert my fibers which is represented in .mat file in
>>> order to be represented on mitk view?
>>> i.e., I'd like to view my data as :
>>> http://www.dkfz.de/de/mbi/images/neuro3.jpg
>>> Note that my .mat file consists of [n] number of fibers which each fiber
>>> [i] consists of number of points [j] like this:
>>>
>>> fibers[n]
>>> |
>>> |__fiber-i__
>>> |
>>> |___point-j(x,y,z)
>>>
>>>
>>>
>>> Please don't hesitate to ask if a further explanation is required ...
>>> Anyway, any information/ method would be very appreciated!
>>> Miri
>>>
>>>
>>> --
>>> Dipl.-Inform. Peter Neher
>>> German Cancer Research Centre
>>> (DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft,
>>> Stiftung des öffentlichen Rechts)
>>> Division of Medical and Biological Informatics
>>> Im Neuenheimer Feld 280, D-69120 Heidelberg
>>>
>>> Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
>>> E-Mail: [email protected]<mailto:[email protected]>,
>>> Web: www.dkfz.de<http://www.dkfz.de/>
>>>
>>> The information contained in this message may be confidential and
>>> legally protected under applicable law. The message is intended solely for
>>> the addressee(s). If you are not the intended recipient, you are hereby
>>> notified that any use, forwarding, dissemination, or reproduction of this
>>> message is strictly prohibited and may be unlawful. If you are not the
>>> intended recipient, please contact the sender by return e-mail and destroy
>>> all copies of the original message.
>>>
>>>
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>>> --
>>> Dipl.-Inform. Peter Neher
>>> German Cancer Research Centre
>>> (DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft,
>>> Stiftung des öffentlichen Rechts)
>>> Division of Medical and Biological Informatics
>>> Im Neuenheimer Feld 280, D-69120 Heidelberg
>>>
>>> Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
>>> E-Mail: [email protected]<mailto:[email protected]>,
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>>> The information contained in this message may be confidential and
>>> legally protected under applicable law. The message is intended solely for
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>>> notified that any use, forwarding, dissemination, or reproduction of this
>>> message is strictly prohibited and may be unlawful. If you are not the
>>> intended recipient, please contact the sender by return e-mail and destroy
>>> all copies of the original message.
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>>
>>
>>
>
>
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