[Insight-users] exclude pixel values (background) from metrics
Luis Ibanez
luis.ibanez at kitware.com
Thu Mar 18 19:06:45 EDT 2010
Hi Darren,
Yeap, something is wrong with the assumption
of the image intensities distribution.
You may also want to generate a histogram for
that image.
The following examples may be useful:
Insight/Examples/Statistics
ImageHistogram1.cxx
ImageHistogram2.cxx
ImageHistogram3.cxx
ImageHistogram4.cxx
Regards,
Luis
----------------------------------------------------------------------------
On Thu, Mar 18, 2010 at 7:02 PM, Darren Weber
<darren.weber.lists at gmail.com> wrote:
>
> Hi Luis et al.,
>
> I'm puzzled by the intensityThreshold, because the optimizer observer gives:
>
> Using fixed image intensity threshold: 1
>
> 0 nan [nan, nan, nan]
> 1 nan [nan, nan, nan]
> 2 nan [nan, nan, nan]
> 3 nan [nan, nan, nan]
> 4 nan [nan, nan, nan]
> 5 nan [nan, nan, nan]
> 6 nan [nan, nan, nan]
> 7 nan [nan, nan, nan]
> 8 nan [nan, nan, nan]
> 9 nan [nan, nan, nan]
> 10 nan [nan, nan, nan]
> 11 nan [nan, nan, nan]
> 12 nan [nan, nan, nan]
> 13 nan [nan, nan, nan]
> 14 nan [nan, nan, nan]
> 15 nan [nan, nan, nan]
> 16 nan [nan, nan, nan]
> 17 nan [nan, nan, nan]
> 18 nan [nan, nan, nan]
> 19 nan [nan, nan, nan]
> 20 nan [nan, nan, nan]
>
>
> I'll try to explore a little more using the
>
> BinaryThresholdImageFilter
>
> I'll take a look at
>
> examples/Filtering/BinaryThresholdImageFilter.cxx
>
> Thanks,
> Darren
>
>
>
> On Wed, Mar 17, 2010 at 3:44 PM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Darren,
>>
>> Excellent,
>>
>> In that case you should be able to eliminate the background
>> by using:
>>
>> intensityThreshold = 1;
>> metric->SetFixedImageSamplesIntensityThreshold( intensityThreshold );
>>
>> If you want to be 100% sure, it may be worth running a
>> BinaryThresholdImageFilter first and saving the output
>> for further visualization. That will provide a good sanity
>> check.
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>> ------------------------------------------------------------------------------------------
>> On Wed, Mar 17, 2010 at 5:22 PM, Darren Weber
>> <darren.weber.lists at gmail.com> wrote:
>> >
>> > Hi Luis et al.,
>> >
>> > I've created the input images by exporting from Photoshop with a defined
>> > background value (RGB: 0 0 0). It's these values that I want to exclude
>> > from the metric in the image registration method.
>> >
>> > The min color is confirmed by the identify program of ImageMagick:
>> >
>> > Colorspace: RGB
>> > Depth: 16-bit
>> > Channel depth:
>> > gray: 16-bit
>> > Channel statistics:
>> > Gray:
>> > min: 0 (0)
>> > max: 46335 (0.707027)
>> > mean: 25664.6 (0.391617)
>> > standard deviation: 15257.7 (0.232818)
>> > kurtosis: -0.857968
>> > skewness: -0.771191
>> >
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