[Insight-users] skull stripping

[U Yakubov]

Hi All,

I would like to use ConnectedThresholdImageFilter for Skull stripping for CT
images. ConnectedThresholdImageFilter requires three parameters: seed, low
and high threshold. I would like that all process will be fully automated.

I found how to get seedX, seedY and seedZ for ConnectedThresholdImageFilter.
I can use Max value of GradientMagnitudeImageFilter, because bones in CT
have very high intensities. My question how to get low threshold.

Any help will be appreciated.

Thanks,

U.


On Fri, Jun 17, 2011 at 11:00 AM, U Yakubov <uyakubov007 at gmail.com> wrote:

> Hi Luis,
>
> For the segmentation of the bones, I used ConnectedThresholdImageFilter
> giving manually 3D coordinates of the seed, low and high threshold of the
> bone intensities. After that I used MaskNegatedImageFilter for the
> separation of the brain. I don't understand why do I need to use distance
> maps to separate the brain? I would like to automate the process. How I can
> find seed and threshold intensities automatically. Is there a way to do
> this?
>
> Thanks,
>
> Uril.
>
>
>
>
>
> On Thu, May 26, 2011 at 1:14 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>
>> Hi U.
>>
>> Skull Stripping on CT should be easier, given that
>> bone has a very high signature in Hounsfield units.
>>
>> You could first segment the skull bone, and then
>> use distance maps to separate the brain.
>>
>>
>>     Luis
>>
>>
>> --------------------------------------------
>> On Tue, May 24, 2011 at 1:17 PM, U Yakubov <uyakubov007 at gmail.com> wrote:
>> > Hi Luis,
>> >
>> > Skull stripper that you mentioned below works for MR images. What about
>> CT
>> > images?
>> >
>> > Thanks,
>> >
>> > U.
>> >
>> > On Sat, May 21, 2011 at 1:53 PM, Luis Ibanez <luis.ibanez at kitware.com>
>> > wrote:
>> >>
>> >> Hi U,
>> >>
>> >> You may find this useful:
>> >>
>> >>
>> >>   http://svn.na-mic.org/NAMICSandBox/trunk/SkullStripper/
>> >>
>> >>
>> >>
>> http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration
>> >>
>> >>
>> http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule
>> >>
>> >>
>> >> They are based on ITK.
>> >>
>> >>
>> >>    Luis
>> >>
>> >>
>> >> ---------------------------------------------------
>> >> On Fri, May 20, 2011 at 3:49 PM, U Yakubov <uyakubov007 at gmail.com>
>> wrote:
>> >> > Hi experts,
>> >> >
>> >> > Does anyone now how to make skull stripping from MRI and CT images
>> using
>> >> > itk
>> >> > software.
>> >> >
>> >> > Thanks,
>> >> >
>> >> > U
>> >> >
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>
>
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