[ITK-users] [ITK] Whole body Segmentation-Identification

[Nicolas Gallego]

Hi Bumpy,
It seams that your problem is exploratory and will get benefit of manual
interaction. Have you tried visualizing your images in ITKSnap for example?
There are tools to do manual segmentation there.
Hope that helps

Nicolás Gallego-Ortiz
Université catholique de Louvain, Belgium


2014-08-01 15:47 GMT+02:00 Bumpy RG <rg.bumpy at gmail.com>:

> Dear All,
>
> I have a dicom series having whole body image sequences, starting from
> head up to legs.
>
> My aim is to write an algorithm to automatically identify the body parts
> (lungs, spines, head etc.) from the dicom sequence.
>
> Although I am very new to the ITK world, I am following these steps in ITK
> (*I would appreciate if you comment whether I am following correct idea
> or not*):
>
>    1. Read dicom series using 'DicomSeriesReadImageWrite2.cxx ' to create
>    a 3D volume and save the result in mhd format.
>    2. Use 'ImageReadRegionOfInterestWrite.cxx' for separating various
>    parts (like left lung, right lung, spines, head etc.) and save them in
>    respective 3D volumes in mhd format.
>    3. Pick the various body parts prepared above, one by one and segment
>    them using robust algorithm (say
>    ThresholdSegmentationLevelSetImageFilter.cxx).
>    4. Use Mathematical Morphology to get better results.
>    5. Using the various results from above, form an algorithm for
>    identifying the various body parts.
>
> Currently I am stuck in the second step because it is so hard to choose
> the co-ordinates for selecting proper region of interest.
>
> For example,  I chose these points for ROI of right lung (I checked the
> co-ordinates using 3D slicer visualizer) and it does not give me good
> results :
> start[0] = 255;
> start[1] =165;
> start[2] = 0;
>
> *However I do not understand how to choose the points properly in ITK.*
>
>
> I would be really glad to have your response.
>
> Thanking you in advance.
> Kind Regards,
> Bumpy.
>
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