Hi All, <br><br>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. <br>
<br>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.<br>
<br>Any help will be appreciated.<br><br>Thanks,<br><br>U.<br><br><br><div class="gmail_quote">On Fri, Jun 17, 2011 at 11:00 AM, U Yakubov <span dir="ltr"><<a href="mailto:uyakubov007@gmail.com">uyakubov007@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Luis,<br><br>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?<br>
<br>Thanks,<br><br>Uril.<div><div></div><div class="h5"><br><br><br><br><br><div class="gmail_quote">On Thu, May 26, 2011 at 1:14 PM, Luis Ibanez <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi U.<br>
<br>
Skull Stripping on CT should be easier, given that<br>
bone has a very high signature in Hounsfield units.<br>
<br>
You could first segment the skull bone, and then<br>
use distance maps to separate the brain.<br>
<br>
<br>
Luis<br>
<br>
<br>
--------------------------------------------<br>
<div><div></div><div>On Tue, May 24, 2011 at 1:17 PM, U Yakubov <<a href="mailto:uyakubov007@gmail.com" target="_blank">uyakubov007@gmail.com</a>> wrote:<br>
> Hi Luis,<br>
><br>
> Skull stripper that you mentioned below works for MR images. What about CT<br>
> images?<br>
><br>
> Thanks,<br>
><br>
> U.<br>
><br>
> On Sat, May 21, 2011 at 1:53 PM, Luis Ibanez <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>><br>
> wrote:<br>
>><br>
>> Hi U,<br>
>><br>
>> You may find this useful:<br>
>><br>
>><br>
>> <a href="http://svn.na-mic.org/NAMICSandBox/trunk/SkullStripper/" target="_blank">http://svn.na-mic.org/NAMICSandBox/trunk/SkullStripper/</a><br>
>><br>
>><br>
>> <a href="http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration" target="_blank">http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration</a><br>
>><br>
>> <a href="http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule" target="_blank">http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule</a><br>
>><br>
>><br>
>> They are based on ITK.<br>
>><br>
>><br>
>> Luis<br>
>><br>
>><br>
>> ---------------------------------------------------<br>
>> On Fri, May 20, 2011 at 3:49 PM, U Yakubov <<a href="mailto:uyakubov007@gmail.com" target="_blank">uyakubov007@gmail.com</a>> wrote:<br>
>> > Hi experts,<br>
>> ><br>
>> > Does anyone now how to make skull stripping from MRI and CT images using<br>
>> > itk<br>
>> > software.<br>
>> ><br>
>> > Thanks,<br>
>> ><br>
>> > U<br>
>> ><br>
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</div></div></blockquote></div><br>
</div></div></blockquote></div><br>