[Insight-users] Re: CVS checkout

[Mathieu Malaterre]

Jessica,

	When did you do this update ? Because ResampleImageFilter6.cxx is only 
2 days old. Could you please do a :

	$cvs update

(in the Insight directory)
Then go in 'Insight/Examples/Filtering/' you should find it here.

Thanks
Mathieu

Jessica de Ryk wrote:
> I tried getting the filter from CVS. As I am a user I used this command to
> get the checkout.
> cvs -d:pserver:anoncvs at www . itk . org/cvsroot/Insight co Insight
> 
> Unfortunately the version I got doen't contain the
> itkVectorResampleImageFilter or the related example,
> ResampleImageFilter6.cxx
> 
> Do I need a different CVS command to get the newest update?
> Thanks again
> Jessica
> 
> 
> 
> ----- Original Message ----- 
> From: "Luis Ibanez" <luis . ibanez at kitware . com>
> To: <jessica-deryk at uiowa . edu>
> Cc: <insight-users at itk . org>
> Sent: Friday, December 12, 2003 2:09 PM
> Subject: Re: [Insight-users] Re: Images Posted
> 
> 
> 
>>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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk . org
>>>http://www . itk . org/mailman/listinfo/insight-users
>>>
>>
>>
>>
> 
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