[Insight-developers] preprocessing for ImageSeriesReader?

[Bradley Lowekamp]

Hello Richard,

This really does sounds like a good use of streaming. Why does streaming not meet your needs? 

I have processed the entire visible human data-set on 32-bit systems this way. It works very well. It usually goes as follows:

ImageSeriesReader
CropImageFIlter
RecursiveGaussianImageFilter (X)
RecursiveGaussianImageFilter (Y)
ShrinkImageFilter
StreamingImageFilter (set the number of updates to the number of slices )

If you are interested in this approach, I may be able to convert my code to an example.

Bills approach will also work, but will require a little more manual pipeline manipulation. Were as with streaming you must ensure that the filter correctly supports streaming. I will admit I am biased towards streaming.

Good luck,
Brad

On May 7, 2010, at 7:57 AM, Richard Beare wrote:

> Hi,
> I don't think this is a job for slice by slice or streaming filters. I
> have a large number of slices that I need to convert to a 3D image.
> However each slice needs to go through a couple of steps. I can do
> this by writing each new images for each slice and then using the
> SeriesReader in the normal way. However I'd like to try to optimize
> the process by integrating everything. It isn't a big deal if it isn't
> possible, but it would be cute to try the integrated approach.
> 
> On Fri, May 7, 2010 at 1:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello,
>> 
>> Is is possible that you are looking to perform out-of-core / streaming
>> processing? Or there is the SliceBySliceImageFilter in memory is not an
>> issue.
>> Brad
>> 
>> 
>> 
>> 
>> On May 4, 2010, at 2:04 AM, Richard Beare wrote:
>> 
>> Hi,
>> I was wondering whether there might be a trick that would allow a
>> slice based preprocessing pipeline to be attached to an image series
>> reader. My particular example is cropping and scaling of each slice
>> before assembling a 3D volume. Perhaps assembling a special slice
>> reader is the way to go? Any other C++ tricks that might work?
>> 
>> Thanks
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>> ========================================================
>> 
>> Bradley Lowekamp
>> 
>> Lockheed Martin Contractor for
>> 
>> Office of High Performance Computing and Communications
>> 
>> National Library of Medicine
>> 
>> blowekamp at mail.nih.gov
>> 
>>