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]> 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]> 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]
>> > 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]
>>> > 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::TractsToProbabilityImageFilter in
>>>> Modules/DiffusionImaging/Algorithms?
>>>>
>>>>
>>>>
>>>> Best
>>>>
>>>> Klaus
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *Von:* Hila Hiler [mailto:[email protected] <[email protected]>]
>>>> *Gesendet:* Donnerstag, 15. März 2012 12:54
>>>> *An:* Neher, Peter
>>>> *Cc:* [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]>
>>>> Date: Sat, Mar 10, 2012 at 10:10 PM
>>>> Subject: need advice: measurement of density of fibers
>>>> To: [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], 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 original message.
>>>
>>>
>>
>
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