Hi Andriy,<br><br>Sorry for repeating this email to you, but I previously had forgotten to carbon copy the Insight users mailing list.<br><br>Thanks,<br>john<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">John Drozd</b> <span dir="ltr"><<a href="mailto:john.drozd@gmail.com">john.drozd@gmail.com</a>></span><br>Date: Fri, Nov 13, 2009 at 4:09 PM<br>Subject: Re: [Insight-users] statistical volume measurement of segmented ventricles<br>
To: Andriy Fedorov <<a href="mailto:fedorov@bwh.harvard.edu">fedorov@bwh.harvard.edu</a>><br><br><br>Thanks Andriy. I have an automated segmentation routine developed that segments the ventricles. I will use the ITK classes to automatically label map this segmentation and then use the label statistics module that you described to give the volume statistics. However, I will also be creating a command line version to process lots of MRI images in which I will find the ITK classes useful, and use 3D Slicer for interactive visual correction. That's my plan.<br>
<font color="#888888">
<br>John</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Fri, Nov 13, 2009 at 3:54 PM, Andriy Fedorov <span dir="ltr"><<a href="mailto:fedorov@bwh.harvard.edu" target="_blank">fedorov@bwh.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>On Fri, Nov 13, 2009 at 15:49, John Drozd <<a href="mailto:john.drozd@gmail.com" target="_blank">john.drozd@gmail.com</a>> wrote:<br>
> Thanks Andriy. I will be developing my ITK code to work as a module within<br>
> 3D Slicer.<br>
><br>
<br>
</div>John,<br>
<br>
This is great!<br>
<br>
One thing you might want to consider is that 3D Slicer already has the<br>
capability to provide you statistics like mm^3 volume for a label. See<br>
the documentation here:<br>
<br>
<a href="http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelStatistics-Documentation-3.4" target="_blank">http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelStatistics-Documentation-3.4</a><br>
<br>
I just don't want you to spend time re-implementing existing<br>
functionality.... Please post to slicer mail list if you need any help<br>
regarding 3D Slicer module development.<br>
<font color="#888888"><br>
Andriy Fedorov<br>
</font><div><div></div><div><br>
<br>
<br>
<br>
> Thanks,<br>
> john<br>
><br>
> On Fri, Nov 13, 2009 at 12:17 PM, Andriy Fedorov <<a href="mailto:fedorov@bwh.harvard.edu" target="_blank">fedorov@bwh.harvard.edu</a>><br>
> wrote:<br>
>><br>
>> > I had previously been using the ITK that came with the 3DSlicer<br>
>> > download, 3D<br>
>> > Slicer Version 3.4 RC1 1.0 (3D Slicer Version 3.4 RC11.0), which did not<br>
>> > have these classes in its Slicer3-lib/Insight/Code/Review directory.<br>
>> ><br>
>> > Now, I have the impetus to use the latest 3.16.0 version of ITK.<br>
>> ><br>
>><br>
>> Hi John,<br>
>><br>
>> 3D Slicer 3.4 is using ITK 3.14, that's why you didn't see the<br>
>> classes. If you check out the current trunk source code for Slicer (or<br>
>> get a recent nightly build) it is using the latest ITK 3.16. The<br>
>> instructions on building Slicer from source are available here<br>
>><br>
>><br>
>> <a href="http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions#Building_the_latest_development_version" target="_blank">http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions#Building_the_latest_development_version</a><br>
>><br>
>> Just FYI in case you would like to develop your tools within 3D Slicer.<br>
>><br>
>> Andriy Fedorov<br>
>><br>
>> > Thanks to both of you again,<br>
>> > john<br>
>> ><br>
>> > On Fri, Nov 13, 2009 at 11:20 AM, Bill Lorensen<br>
>> > <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>>wrote:<br>
>> ><br>
>> >> John,<br>
>> >><br>
>> >> The classes in Gaetan's paper now reside in the Insight/Code/Review.<br>
>> >><br>
>> >> Bill<br>
>> >><br>
>> >> On Fri, Nov 13, 2009 at 4:29 AM, John Drozd <<a href="mailto:john.drozd@gmail.com" target="_blank">john.drozd@gmail.com</a>><br>
>> >> wrote:<br>
>> >> > Thank you very much. This is very helpful.<br>
>> >> ><br>
>> >> > john<br>
>> >> ><br>
>> >> > On Thu, Nov 12, 2009 at 3:42 PM, C.Cagatay Bilgin <<a href="mailto:bilgic@cs.rpi.edu" target="_blank">bilgic@cs.rpi.edu</a>><br>
>> >> wrote:<br>
>> >> >><br>
>> >> >> I use the following submission by Gaetan for<br>
>> >> >> that purpose. Note that It has way more<br>
>> >> >> morphological features than you asked for.<br>
>> >> >><br>
>> >> >> <a href="http://www.insight-journal.org/browse/publication/176" target="_blank">http://www.insight-journal.org/browse/publication/176</a><br>
>> >> >><br>
>> >> >> Regards,<br>
>> >> >><br>
>> >> >><br>
>> >><br>
>> >> ----------------------------------------------------------------------------<br>
>> >> >> Cemal Cagatay Bilgin,<br>
>> >> >> Ph.D Candidate in Computer Science Department at RPI<br>
>> >> >> <a href="mailto:bilgic@cs.rpi.edu" target="_blank">bilgic@cs.rpi.edu</a> -<br>
>> >> >> <a href="http://www.cs.rpi.edu/%7Ebilgic" target="_blank">http://www.cs.rpi.edu/~bilgic</a><<a href="http://www.cs.rpi.edu/%7Ebilgic" target="_blank">http://www.cs.rpi.edu/%7Ebilgic</a>><br>
>> >> >> Lally 01A, 110 8th Street Troy, NY 12180-3590, USA.<br>
>> >> >> Tel: (518) 276-8489, Fax:(518) 276-4033<br>
>> >> >><br>
>> >> >> On Nov 12, 2009, at 12:31 PM, John Drozd wrote:<br>
>> >> >><br>
>> >> >>> Hello,<br>
>> >> >>><br>
>> >> >>> Using Examples/Segmentation/ConnectedThresholdImageFilter.cxx,<br>
>> >> >>> I successfully segmented ventricles from an mri image of a human<br>
>> >> >>> brain.<br>
>> >> >>><br>
>> >> >>> Using ITK, I would like to calculate the statistical volume in mm^3<br>
>> >> >>> of<br>
>> >> >>> these segmented ventricles.<br>
>> >> >>> Are there any ITK functions that will allow me to calculate the<br>
>> >> >>> volume<br>
>> >> of<br>
>> >> >>> a segmented region?<br>
>> >> >>><br>
>> >> >>> Thanks,<br>
>> >> >>> John<br>
>> >> >>> _____________________________________<br>
>> >> >>> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>> >> >>><br>
>> >> >>> Visit other Kitware open-source projects at<br>
>> >> >>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >> >>><br>
>> >> >>> Kitware offers ITK Training Courses, for more information visit:<br>
>> >> >>> <a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br>
>> >> >>><br>
>> >> >>> Please keep messages on-topic and check the ITK FAQ at:<br>
>> >> >>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>> >> >>><br>
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>> >> ><br>
>> >> ><br>
>> >> > _____________________________________<br>
>> >> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>> >> ><br>
>> >> > Visit other Kitware open-source projects at<br>
>> >> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >> ><br>
>> >> > Kitware offers ITK Training Courses, for more information visit:<br>
>> >> > <a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br>
>> >> ><br>
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><br>
><br>
</div></div></blockquote></div><br>
</div></div></div><br>