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

[Luis Ibanez]

On Thu, Jan 28, 2010 at 4:01 PM, Isaac Abbott <isaac.abbott at gmail.com> wrote:
> I would appreciate an example of a pipeline used of a large dataset (like
> Visual Human).
> Thanks,
> Isaac
>
--------------------------------------------------------------------------


Hi Isaac,

You will find it in the April 2009 issue of "The Source":

"IO Streaming in ITK"
http://www.kitware.com/products/archive/kitware_quarterly0409.pdf
by Brad Lowekamp


pages 5-7


     Regards,


             Luis


--------------------------------------
> 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)
>>> >
>>> >
>>
>
>