Hi Miri,
by default I apply a fiber smoothing for example after a successful
tracking. Just looks nicer :) Also for some postprocessing steps like
TDI generation fiber resampling/smoothing is used to ensure correct
processing of the bundle, but this is done inside the respective filter.
The fiber processing view allows you to smooth the fibers via the GUI.
You can also smooth your fibers via a Kochanek spline interpolation by
calling DoFiberSmoothing an your fiber bundle.
And yes, thats how the writer input is specified:
vtkSmartPointer<vtkPolyDataWriter> writer =
vtkSmartPointer<vtkPolyDataWriter>::New();
writer->SetInput(fiberBundleX->GetFiberPolyData());
writer->SetFileName("myFileName.fib");
writer->SetFileTypeToASCII();
writer->Write();
For reading and writing fibers you can also have a look at the
mitkFiberBundleXReader/Writer files.
Best
Peter
On 15.02.2012 17:33, Miri Trope wrote:
Hi Peter,
Yes, now it's working :-)
So after I've created a FiberBundleX structure,
would you recommend ,from your experience, further methods to increase
in quality that fiberBundle structure (smoothing etc.)
BTW,
does the writing operate by vtkPolyDataWriter like this?
writer_pd->SetInput(fiberBundleX->GetFiberPolyData());
Regards,
Miri
On Wed, Feb 15, 2012 at 2:40 PM, Peter Neher
<[email protected] <mailto:[email protected]>> wrote:
Hi Miri,
maybe you have alpready seen it in the other diffusion related
mail Sascha just answered. The module is called
"MitkDiffusionImaging" not "DiffusionImaging". I think the rest
looks good. So if you activate all the diffusion modules via cmake
and include this dependency in your cmakelists.txt it should work
fine.
Best
Peter
On 14.02.2012 17:40, Miri Trope wrote:
Regarding section1 which I wrote:
I intended to write: DiffusionImaging (not ImageDiffusion).
- I'd like to mention that this directory is actually exist in
the same location as all the other dependencies that I've mentioned.
Best,
Miri.
On Tue, Feb 14, 2012 at 4:59 PM, Miri Trope <[email protected]
<mailto:[email protected]>> wrote:
Hi Peter,
OK, I thought that it's a repeating question.
So, here is the process with the corresponding errors:
After the build process, I just changed the codes of
awesomeProject (filter and plug-in) to mine, and tried to do
these things:
1) add a dependency to my MyAwesomeLib:
DEPENDS Mitk MitkExt Qmitk SceneSerialization ImageDiffusion
but it returned the error:
Module MyAwesomeLib won't be built, missing dependency:
DiffusionImaging
2) include at my filter's header the header (without that
dependency):
#include "mitkFiberBundleX.h"
but it returned an error:
A\mitk-superbuild\mitk-build\mitk-projecttemplate\modules\myawesomelib\AwesomeImageFilter.h(34)
: fatal error C1083: Cannot open include file:
'mitkFiberBundleX.h': No such file or directory
3) this command returned the error: (that header wasn't
included):
mitk::FiberBundleX::Pointer fiberBundle =
mitk::FiberBundleX::New(fiberPD);
A\MITK-ProjectTemplate\Modules\MyAwesomeLib\AwesomeImageFilter.cpp(62)
: error C3083: 'FiberBundleX': the symbol to the left of a
'::' must be a type
Thank you for reading until the end :-)
Best,
Miri
On Tue, Feb 14, 2012 at 1:15 PM, Peter Neher
<[email protected]
<mailto:[email protected]>> wrote:
Hi Miri,
it would be better to send all your questions directly to
the mailinglist so that other members can also help or
profit from the conversation.
Regarding your problem, I am not sure what exactly
"doesn't work" mean. mitk::FiberBundleX is actually not a
filter but a datatype. Does the sample code I sent you
compile or are there any errors?
Best,
Peter
On 11.02.2012 21:56, Miri Trope wrote:
Hi Peter,
Regarding this filter which you have suggested:
_*mitk::FiberBundleX*_
What I should do in order to make that work?
What I've done:
- installed DiffusionImaging module.
- inserted: #include "mitkFiberBundleX.h"
- tried to add a dependency 'DiffusionImaging' in the
CMakeList.txt but it doesn't work.
I guess there are other things which I missed?...
Best Regards,
Miri
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
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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
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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 the
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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.
--
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.
--
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], Web: 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
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