Hi Hila,
we use the upsampling to ensure that no voxel that is crossed by a fiber
is left out. This might happen if the distance between two points on the
fiber is too large. And as said in my previous email, the filter does
not calculate the number of fibers per voxel. But if desired it could
easily be redesigned to do so. Just visit each voxel only once per fiber
and skip the normalization step.
Regarding the runtime error you encountered, could you ad a bug to our
bugtracker and upload the according .fib needed to reproduce the bug? I
will have a look at it in the next couple of days.
Best
Peter
On 21.03.2012 10:58, Hila Hiler wrote:
In addition,
I investigated the code of itkTractDensityImageFilter and wondered :
why is the up-sampling necessary ? I guess that the connection between
density and upsampling isn't comprehensible for me. and however, how
is the sampling correlated to your algorithm description (that
measures number of fibers per a voxel)?
any information or links to data sources would be very helpful.
Best,
Hila
On Tue, Mar 20, 2012 at 10:45 AM, Hila Hiler <[email protected]
<mailto:[email protected]>> wrote:
I'm starting to wonder whether the data of fibers that inserted is
incorrect, although I generated the .fib file as suggested.
And the bar "fiber bundle statistics" presents:
fibers
Number of fibers: 10000
Mean fiber length: 7.01857cm
Median fiber length: 6.93052cm
Standard deviation: 5.39865cm
But still I got that run time error that is illustrated in the
attached file.
now I can't do nothing with this module because the same error
represented in each application...
What's the reason for this?
Regards,
Hila
On Mon, Mar 19, 2012 at 10:44 AM, Hila Hiler <[email protected]
<mailto:[email protected]>> wrote:
Thank you Peter.
I tried to use the GUI in order to generate a density image
but I encountered with a run time error that indicates about
an access violation reading location in:
vtkIdType GetNumberOfPoints() {return
this->Data->GetNumberOfTuples();}
any ideas?
On Sun, Mar 18, 2012 at 10:24 AM, Peter Neher
<[email protected]
<mailto:[email protected]>> wrote:
Dear Hila,
we basically walk along the fiber and increase the grey
value of each encountered voxel. Afterwards everything is
normalized to one. So you don't get absolute values how
many fibers are passing each voxel but an indicator of
where are many and where are only few fibers in the image.
The filter is called in
QmitkFiberProcessingView::GenerateTractDensityImage so you
can use that as a reference. The simplest example would be
the following:
itk::TractDensityImageFilter< float >::Pointer generator =
itk::TractDensityImageFilter< float >::New();
generator->SetFiberBundle(fib);
generator->Update();
where fib is a mitk::FiberBundleX::Pointer.
Best
Peter
On 16.03.2012 18:28, Hila Hiler wrote:
Thank you!
would you please explain :
- how this filter works (a brief description of the
algorithm) ?
- example of how to use this filter ? (which inputs to
insert, how to get the output ...)
many thanks in advance ...
Best,
Hila
On Thu, Mar 15, 2012 at 6:32 PM, Peter Neher
<[email protected]
<mailto:[email protected]>> wrote:
Actually I recently changed the name to
itk::TractDensityImageFilter.
On 15.03.2012 13:20, Fritzsche, Klaus H. wrote:
Dear Hila,
die you see the
itk::TractsToProbabilityImageFilterin
Modules/DiffusionImaging/Algorithms?
Best
Klaus
*Von:*Hila Hiler [mailto:[email protected]]
*Gesendet:* Donnerstag, 15. März 2012 12:54
*An:* Neher, Peter
*Cc:* [email protected]
<mailto:[email protected]>
*Betreff:* [mitk-users] Fwd: need advice:
measurement of density of fibers
Dear Peter, Mitk's users
Would you please consider my question?
any ideas/thoughts would be very appreciated!
It's obvious that the density equation is:
[samples/volume]*[samples/fiber]
but I'm afraid it's not the right aspect to this
challenge.
maybe the bundle color’s gradients can provide any
helpful details?
Best,
Hila
---------- Forwarded message ----------
From: *Hila Hiler* <[email protected]
<mailto:[email protected]>>
Date: Sat, Mar 10, 2012 at 10:10 PM
Subject: need advice: measurement of density of fibers
To: [email protected]
<mailto:[email protected]>
Hi all,
How I can calculate the fibers density from a
.fib/.vtk 3d image ?
I thought to calculate it along it's direction of
longitude.
maybe I should consider to calculate the number of
fibers which are crossing an orthogonal plane?
another q: how I can achieve the gradient value
which is represented as a color on the .fib file?
--
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
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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], 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
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
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