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]>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]> 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]>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]>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], 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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>>>
>>> --
>>> 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.
>>>
>>>
>>
>
> --
> 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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