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. ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ mitk-users mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/mitk-users -- 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. ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2_______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
