[Insight-users] Re: Images Posted

[Bill Lorensen]

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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