[Insight-users] Re: Images Posted

[Jessica de Ryk]

I have been using version 1.4 downloaded as a zip from the webste. If I use
CVS will i have to download the complete itk source again??
Thanks
Jessica



----- Original Message ----- 
From: "Bill Lorensen" <wlorens1 at nycap . rr . com>
To: "Luis Ibanez" <luis . ibanez at kitware . com>; <jessica-deryk at uiowa . edu>
Cc: <insight-users at itk . org>
Sent: Saturday, December 13, 2003 9:44 AM
Subject: Re: [Insight-users] Re: Images Posted


> Jessica,
> There was a bug on the new filter. If you updated yesterday, please do so
> again today,
>
> Bill
>
> At 03:09 PM 12/12/2003, Luis Ibanez wrote:
> >Hi Jessica,
> >
> >ITK was missing a filter for resampling RGB images,
> >which is one of the steps required for your program.
> >
> >We just added a new filter:
> >
> >         itkVectorResampleImageFilter
> >
> >Please update your CVS checkout in order to get this
> >filter. You will find and example on how to use this
> >filter in the file:
> >
> >
> >   Insight/Examples/Filtering/ResampleImageFilter6.cxx
> >
> >
> >Please use this filter intead of the plain itkResampleImageFilter
> >in order to resample your RGB images.
> >
> >Note that you don't need 3 dimensions. In ITK the notion
> >of color channels is represented using the RGBPixel class.
> >You simply need a 2D image of RGBpixels, like:
> >
> >
> >    typedef    itk::RGBPixel< unsigned char >   PixelType;
> >    typedef    itk::Image< PixelType, 2 >       ImageType;
> >
> >
> >Please let us know if you find any problems,
> >
> >
> >Thanks
> >
> >
> >   Luis
> >
> >
> >------------------------------------
> >jessica-deryk at uiowa . edu wrote:
> >
> >>I am composing a mosaic of many small 2D RGB image tiles to make a
single
> >>image of a complete slice of lung. The images are stereomicroscopic not
> >>confocal (but one day the system will hopefully use confocal). A 3D
> >>reconstruction of the tissue will be generated from the many 2D slices
> >>and the resulting pathology dataset registered with corrosponding CT
images.
> >>I do just need to resample the RGB image. I thought I might have needed
> >>three dimensions (for the three channels) I guess i never tried
> >>resampling the RGB images with the 2D resample.
> >>If i use the ImageReadWrite example, is there a way inwhich I can
specify
> >>my pixel spacing or should I modify the text file once it is generated?
> >>Thanks again
> >>Jessica
> >>Quoting Luis Ibanez <luis . ibanez at kitware . com>:
> >>
> >>>Hi Jessica,
> >>>
> >>>Thanks for posting your images in MyPACS.
> >>>It was pretty easy to look at them.
> >>>
> >>>I'm confused now if you are using 3D images
> >>>like in confocal microscopy or you are just
> >>>composing the mosaic of a large image by
> >>>stitching the tiles in rows and columns
> >>>in a 2D grid. Could you please clarify this ?
> >>>
> >>> From your last email it looks like you just
> >>>need to resample the RGB 2D image...
> >>>is that right ?
> >>>
> >>>----
> >>>
> >>>If you want to convert the images from one format
> >>>to another you can simply use the ITK example
> >>>
> >>>    Insight/Examples/IO/ImageReadWrite.cxx
> >>>
> >>>you can for example read a PNG image and write it
> >>>as Analyze or MetaImage format.
> >>>
> >>>I would suggest you to use MetaImage since the
> >>>header is in ascii text and it is easy to read.
> >>>
> >>>Simply execute the program as:
> >>>
> >>>    ImageReadWrite  input.png   output.mhd
> >>>
> >>>That will convert your input PNG image into
> >>>a MetaImage format. You can also read JPEG
> >>>and TIFF images (if you are using the CVS
> >>>version of ITK).
> >>>
> >>>---
> >>>
> >>>Regards,
> >>>
> >>>
> >>>   Luis
> >>>
> >>>
> >>>----------------------
> >>>Jessica de Ryk wrote:
> >>>
> >>>
> >>>>I have built the adjusted code but am having run time problems when I
> >>>>input my images. I get an abnormal program termination (exception
> >>>>breakpoint) I have posted an example of two images on the MyPACS.net
> >>>>(the case number is 253148)
> >>>>Maybe I am aproaching final output of producing the cropped tile in
> >>>>wrong way? I have many images to tile together to construct a single
> >>>>color slice (the 3D was for the color as opposed to grayscale) of lung
> >>>>pathology. The overlap is 20% of the image FOV + /-some error caused
by
> >>>>inaccuracy in the aquisition system. I want to register two images and
> >>>>then join them to produce one aligned image. Then register the aligned
> >>>>image with the next tile, etc first building up image rows then
> >>>>registering the individual rows. I thought this would be very straight
> >>>>forward to accomplish. As I am much more familiar with C, I thought I
> >>>>could program the organization of the images with respect to
eachother,
> >>>>and the overall tiling of the images and call my itk based
registration
> >>>>program to produced the correctly cropped image tiles.
> >>>>What program would you recomend to convert my images?? Which format is
> >>>>better, Analyze or MetaImage
> >>>>Thanks for your ongoing advice
> >>>>Jessica
> >>>>
> >>>
> >>>
> >>
> >>
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> >
> >
> >
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