[ITK-users] LabelStatisticsImageFilter in 3D

[Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]]

Hi Mathew,

As I haven¹t seen your code I cannot pinpoint the issue, but it is not the
dimension of the image.

The following SimpleITK code does what I believe you are asking for (image
is available here - https://midas3.kitware.com/midas/item/317034):

import SimpleITK as sitk

image = sitk.ReadImage("training_001_ct.mha")

# HU values for bone are 700 and up
segmented_image = image>700

# segmented label for the threshold operation is 1 (0 for everything else).
# the LabelIntensityStatisticsImageFilter also works with multiple labels
and not just a binary segmentation.
segmented_label = 1

lisf = sitk.LabelIntensityStatisticsImageFilter()
lisf.Execute(segmented_image, image)

print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))

     hope this helped

             Ziv






On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:

>Hi
>
>Using SimpleITK I'm trying to get statistics for a grayscale image
>segmentation for which I have a binary mask.  Both image and mask are 3D
>volumes
>
>I have converted my binary mask to a Label map and then tried to apply
>the LabelStatisticsImageFilter, however I get the following exception:
>
>Pixel type: 32-bit float is not supported in 3D
>
>I've tried casting the intensity image to unsigned int, Float 64 etc...
>none of them work.  It seems to be the 3D that is the issue.  Is this
>filter defined for 3D images?  There is nothing I have found in the
>documentation/source to suggest not.
>
>Thanks
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