Hi, thanks for the answer.
I was not precise in my previous mail. Actually, the whole 4D images were saved (not just 3D images as I wrote), but with as many names as the number of timesteps. Both the ".hdr" and the ".img" files were identical for every saved image file. You can merge the fix from here: https://github.com/cim-unito/MITK/branches/fix-saving_4D_Analyze_images Best, Miklos On Thu, Sep 8, 2011 at 8:04 AM, Hering, Jan <[email protected]> wrote: > Hi Miklos, > > inserting further if-condition like the other two will solve your problem. > The ImageWriter checks for .pic or .nrrd file extension at this place, > because of the support for 3D+t like you wrote. You also need to handle > writing of the ".hdr" case few lines below separately, e.g. here > > 215 if(m_Extension.find(".nrrd") ... > > Best, > Jan > > > On Sep 7, 2011, at 7:36 PM, Miklos Espak wrote: > >> I investigated a bit. >> The problem is with the mitkImageWriter.cpp that contains a code >> segment like this: >> >> // If the extension is NOT .pic and NOT .nrrd the following block is entered >> if ( m_Extension.find(".pic") == std::string::npos >> && m_Extension.find(".nrrd") == std::string::npos) >> { >> if(input->GetDimension() > 3) >> { >> int t, timesteps; >> >> timesteps = input->GetDimension(3); >> ... >> >> So 3D+t images are split into 3D images and then saved one by one. >> What is the motivation behind this? I suppose you wanted to split only >> those image formats that do not support 4D images. If yes, I would >> suggest to add the ".hdr" extension to the "if" condition. >> >> Could somebody confirm this? >> >> Thanks, >> Miklos >> >> On Wed, Sep 7, 2011 at 4:45 PM, Miklos Espak <[email protected]> wrote: >>> I see. My case is different then. >>> >>> After that I registered the NiftiImageIOFactory by >>> itk::NiftiImageIOFactory::RegisterOneFactory(); >>> I coul read and write images by the built-in mitk::ItkImageFileReader >>> and mitk::ItkImageFileWriter, respectively. (Even the series reader >>> works.) >>> >>> I mean, this works through the API. Opening a 3D/3D+t image from the >>> GUI also works, the only thing is that I have to choose "all" instead >>> of "known extension" because the ".hdr" extension is not listed. >>> >>> The bigger problem is saving via the datamanager view context menu. >>> Even if saving through API works, when I use the menu item then a >>> series of images is saved, and a warning is displayed about that. >>> >>> I am afraid that this should be fixed in either the menu action or the >>> built-in object factories. I did not debug it, though. >>> >>> Miklos >>> >>> On Tue, Sep 6, 2011 at 11:14 PM, Clarkson, Matt <[email protected]> >>> wrote: >>>> Hi Miklos, >>>> >>>> Using the documents here: http://www.mitk.org/wiki/BugSquashingSeminars, >>>> and specifically the "Defining your own MITK Datatypes" it was quite easy >>>> to create the necessary Factory classes to create a reader for a specific >>>> file format, and to have the file extensions appear in the Load/Save >>>> dialog boxes. >>>> >>>> However, my problem was that I wanted to NOT use the standard ITK Analyze >>>> reader, which meant replacing the mitkItkImageFileReader, and replace it >>>> with a modified version. >>>> This turns out to be a bit trickier, as you would have to unregister the >>>> MITK provided one, and provide your own. >>>> >>>> However, we could just ask for .img and .img.gz to be added to the file >>>> dialog box (via mitkCoreObjectFactory.cpp), as this would probably suffice >>>> for most people, and the image would be read using the standard >>>> mitkImageFileReader.h >>>> >>>> Can you remind me again, why did you have to register a new Nifti file >>>> reader when ITK and hence MITK already had one? >>>> >>>> Matt >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 6 Sep 2011, at 17:09, Miklos Espak wrote: >>>> >>>>> Hi, >>>>> >>>>> if I save a 3D+t image through the GUI (datamanager view context >>>>> menu), a series of images is saved instead of a single image. >>>>> >>>>> I would like to use the Analyze format (.hdr + .img), it is not >>>>> offered by the save dialog, so I chose Nifti. >>>>> >>>>> I registered the itk::NiftiImageIOFactory, and from the sources I can >>>>> open and save 3D+t images properly. Is there a way to get around this? >>>>> >>>>> Matt! >>>>> Have you succeeded with adding hdr to the open/save dialog? >>>>> >>>>> Thanks, >>>>> Miklos >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Special Offer -- Download ArcSight Logger for FREE! >>>>> Finally, a world-class log management solution at an even better >>>>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you >>>>> download Logger. Secure your free ArcSight Logger TODAY! >>>>> http://p.sf.net/sfu/arcsisghtdev2dev >>>>> _______________________________________________ >>>>> mitk-users mailing list >>>>> [email protected] >>>>> https://lists.sourceforge.net/lists/listinfo/mitk-users >>>> >>>> >>> >> >> ------------------------------------------------------------------------------ >> Using storage to extend the benefits of virtualization and iSCSI >> Virtualization increases hardware utilization and delivers a new level of >> agility. 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