Hi Daniel,
Thanks for clarifying. Yes, it was a multi-frame MR. We were not using any
advanced (multiframe) feature of the MR & getting the basic images helps us
to complete our tasks. A smart decision taken during implementation of the
reader has helped us now :)
Best Regards,
Arpit
On Tue, Feb 9, 2016, 2:18 PM <[email protected]>
wrote:
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> 1. Re: Possible Bug: Reading Unsupported MR data set (Daniel Maleike)
> 2. Re: Data array visualization (Fetzer, Andreas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 8 Feb 2016 17:50:04 +0100
> From: Daniel Maleike <[email protected]>
> Subject: Re: [mitk-users] Possible Bug: Reading Unsupported MR data
> set
> To: <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Arpit,
>
> without having looked into your data, I suppose that this "Unsupported"
> is due to the multi-frame aspect of your data, i.e. a single DICOM file
> contains multiple image slices. Unless the code has advanced
> significantly, those images are not supported.
>
> When implementing the reader, we were sure that there are many
> multi-frame variants that we are not able to load correctly. Only a
> small portion that contains a single regular stack of images is loaded.
> Because our code cannot tell apart the simple from the complex cases, we
> decided to still return the image if the underlying ITK/GDCM does read
> an image (so the adventurous user/developer could see a result), but
> still not call it supported because we know that this is a lucky case
> among many unlucky ones.
>
> Regards,
> Daniel
>
> On 08.02.2016 15:19, Arpit Paliwal wrote:
> > Dear All,
> >
> > I have faced strange issue with MITK. I was loading MR data set from
> > Phillips.
> > It was shown as unsupported but it still got loaded correctly. I can
> > perform all operations without any issue. What could be the reason of
> > this issue ?
> >
> > Output from MBI log :-
> >
> > 1225.51 core.data.dataNodeFac: DataNodeFactory: Loading DICOM series
> > 0: Series UID 1.3.46.670589.11.80001.5.0.4468.2016011113171902000
> > 1225.51 core.data.dataNodeFac: 23 'MR' files (MR Image Storage)
> > loaded into 1 mitk::Image
> > 1225.52 core.data.dataNodeFac: multi-frame: Yes
> > _*1225.52 core.data.dataNodeFac: reader support: Unsupported*_
> > 1225.52 core.data.dataNodeFac: pixel spacing type: In Patient
> > 1225.53 core.data.dataNodeFac: gantry tilt corrected: No
> > 1225.53 core.data.dataNodeFac: 3D+t: No
> > 1225.53 core.data.dataNodeFac:
> > -------------------------------------------------
> >
> > Link of anonymous DICOM data
> > https://www.dropbox.com/s/6lt96jchtzhtd1k/MR%20Data.zip?dl=0
> >
> > Best Regards,
> > Arpit
> >
> >
> >
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> --
> Dr. Daniel Maleike, Mint Medical GmbH
> Friedrich-Ebert-Stra?e 2, 69221 Dossenheim/Heidelberg
> Gesch?ftsf?hrer: Dr. Matthias Baumhauer, Registergericht Mannheim, HRB
> 709351
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 9 Feb 2016 09:48:20 +0100
> From: "Fetzer, Andreas" <[email protected]>
> Subject: Re: [mitk-users] Data array visualization
> To: "Fitze Thomas (fitz)" <[email protected]>, Rostislav Khlebnikov
> <[email protected]>
> Cc: mitk-users <[email protected]>
> Message-ID: <d2df6176.22365%[email protected]>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Rostislav and Thomas,
>
> it is possible to visualize data arrays in MITK at a low level: You can
> enable scalar visibility for surface / unstructured grid data via the
> PropertyView by checking "scalar visibilty". You can also choose between
> the different scalar arrays via the property "scalar mode". However the
> functionality is pretty limited. You can't change the transfer function or
> select different entries of the data array (afaik simply the first entry is
> used for visualization).
>
> We are definitely interested in extending the functionality for data array
> visualization and would gladly discuss design or collaboration.
> My first thought is, that we should try to keep as much as possible in the
> PropertyView since it's primary purpose is it, to tell MITK how to render
> the data.
>
> Best regards,
> Andreas
>
> Von: "Fitze Thomas (fitz)" <[email protected]<mailto:[email protected]>>
> Datum: Monday 8 February 2016 16:58
> An: Rostislav Khlebnikov <[email protected]<mailto:
> [email protected]>>
> Cc: "[email protected]<mailto:
> [email protected]>" <[email protected]
> <mailto:[email protected]>>
> Betreff: Re: [mitk-users] Data array visualization
>
> Hi Rostislav,
>
> You?re correct that VTK offers the mappers, but there?s no GUI to access
> the functionality in MITK (afaik). I implemented a variation of the
> org.mitk.gui.qt.ugvisualization plugin that offers rudimentary data array
> visualization for unstructured grids. I tried adding transfer function
> editing using the already existing qmitk transfer function generator
> widget, but i couldn?t get it to work properly.
>
> I also tried to get some kind of 2d unstructured grid mappers to work, but
> i didn?t have much success. It?s possible to get a polygon outline, but
> that?s about it. The unstructured grid mappers are kinda sluggish and tend
> to slow down the whole application.
>
> There?s a lot of work to be done to create something similar to ParaView,
> but the effort would be very much appreciated.
>
> Cheers,
> Thomas
>
> [cid:[email protected]]
>
> On 08.02.2016, at 14:57, Rostislav Khlebnikov <
> [email protected]<mailto:[email protected]>>
> wrote:
>
> Hi guys,
>
> I was wondering if there is any work ongoing/planned for visualization
> of data arrays in MITK.
> What I mean by this is, for example, visualization of simulation results
> in a manner similar to ParaView - i.e. selection of data arrays (e.g.
> velocity, pressure, etc.), transfer function editing, etc.
> This would probably include visualization of data on vtkPolyData and
> vtkUnstructuredGrid objects.
>
> I realize that there is some functionality in the corresponding mappers,
> but there's no UI for this yet (or is there?).
>
> Please let me know if there's already some work in this direction and if
> you are interested in such functionality and would like to discuss the
> design/collaboration on this issue.
>
> All best,
> Rostislav.
>
>
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