[Insight-users] Apply filter only on a specific region of very large image ?

[Isaac Abbott]

I would appreciate an example of a pipeline used of a large dataset (like
Visual Human).
Thanks,
Isaac

On Thu, Jan 28, 2010 at 4:00 PM, Isaac Abbott <isaac.abbott at gmail.com>wrote:

> Currently I am using the MedianImageFilter and the
> SmoothingRecursiveGaussianImageFilter or
> HessianRecursiveGaussianImageFilter.
> We also do some other "filtering" using code that is not in the form of an
> itk filter (doesn't use any ITK yet)
>
> This same project requires some visualization of this image - our plan was
> to create a 2D projection and create a sliding box that the is used to
> define the region that is rendered using VTK.
> For this task I also need to just grab a portion of the image at one time
> for creating the projection and for creating the volume.
>
> Isaac
>
>
>
> On Thu, Jan 28, 2010 at 3:48 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>
>> Hi Isaac,
>>
>> As you have already noticed, not all filters are
>> streamable.
>>
>> However, for those that are, it should be possible
>> to process your image by pieces.
>>
>> Brad Lowekamp has recently revamped the streaming
>> pipeline and verified that is possible to pass the entire
>> Visible Human dataset through an ITK pipeline.
>>
>>
>> What specific ITK filters are you using ?
>>
>>
>> If you are having problems with the pipeline, we should
>> identify a reproducible minimal example, in case there
>> is anything that needs to be fixed.
>>
>>
>>    Please let us know,
>>
>>
>>            Thanks
>>
>>
>>
>>                 Luis
>>
>>
>> -----
>> PS. I'm copying the ITK users-list, since this
>> topics will be of interest to many users.
>>
>> --------------------------------------------------------------
>> On Thu, Jan 28, 2010 at 3:43 PM, Isaac Abbott <isaac.abbott at gmail.com>
>> wrote:
>> > Luis,
>> >
>> > I'm trying to process some very large 3D images.  I cannot load these
>> images
>> > using ImageFileReader because I run out of RAM.
>> > I would like to apply various filters to only subregions of this image,
>> and
>> > write the output to the same output image file.
>> >
>> > This means my input and output images might be something like 10,000 x
>> > 10,000 x 200 voxels, but I only want 1000x1000x100 in memory.
>> > I'd load up a region, do the processing, then save the result to file,
>> and
>> > iterate, saving the results to the same file each time.
>> >
>> > I have been following the discussion about applying filters to ROIs of
>> an
>> > itk::Image.
>> > I've also seen some discussion about the usage of buffered region vs
>> largest
>> > possible region vs requested region.
>> > And, I've looked at the StreamingImageFilter - which only seems to work
>> for
>> > a limited subset of the filters.
>> >
>> > None of these discussions seem to meet my need. According to the
>> > documentation I should be able to do something with the buffered region,
>> > because this defines only the region of the image that is in memory -
>> but I
>> > haven't seen this work in practice.
>> >
>> > Thanks for any help you can give,
>> > Isaac (Roysam lab, RPI)
>> >
>> >
>>
>
>
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