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]
<mailto:[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
-------------------------------------------------
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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]><mailto:[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]><mailto:[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
--
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German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der
Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
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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
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E-Mail: [email protected]
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<http://www.dkfz.de><http://www.dkfz.de/>
The information contained in this message may be confidential
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intended solely for the addressee(s). If you are not the
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