[Insight-users] Fwd: statistical volume measurement of segmented ventricles

[John Drozd]

Hi Andriy,

Sorry for repeating this email to you, but I previously had forgotten to
carbon copy the Insight users mailing list.

Thanks,
john

---------- Forwarded message ----------
From: John Drozd <john.drozd at gmail.com>
Date: Fri, Nov 13, 2009 at 4:09 PM
Subject: Re: [Insight-users] statistical volume measurement of segmented
ventricles
To: Andriy Fedorov <fedorov at bwh.harvard.edu>


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.

John


On Fri, Nov 13, 2009 at 3:54 PM, Andriy Fedorov <fedorov at bwh.harvard.edu>wrote:

> On Fri, Nov 13, 2009 at 15:49, John Drozd <john.drozd at gmail.com> wrote:
> > Thanks Andriy. I will be developing my ITK code to work as a module
> within
> > 3D Slicer.
> >
>
> John,
>
> This is great!
>
> One thing you might want to consider is that 3D Slicer already has the
> capability to provide you statistics like mm^3 volume for a label. See
> the documentation here:
>
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelStatistics-Documentation-3.4
>
> I just don't want you to spend time re-implementing existing
> functionality.... Please post to slicer mail list if you need any help
> regarding 3D Slicer module development.
>
> Andriy Fedorov
>
>
>
>
> > Thanks,
> > john
> >
> > On Fri, Nov 13, 2009 at 12:17 PM, Andriy Fedorov <
> fedorov at bwh.harvard.edu>
> > wrote:
> >>
> >> > I had previously been using the ITK that came with the 3DSlicer
> >> > download, 3D
> >> > Slicer Version 3.4 RC1 1.0 (3D Slicer Version 3.4 RC11.0), which did
> not
> >> > have these classes in its Slicer3-lib/Insight/Code/Review directory.
> >> >
> >> > Now, I have the impetus to use the latest 3.16.0 version of ITK.
> >> >
> >>
> >> Hi John,
> >>
> >> 3D Slicer 3.4 is using ITK 3.14, that's why you didn't see the
> >> classes. If you check out the current trunk source code for Slicer (or
> >> get a recent nightly build) it is using the latest ITK 3.16. The
> >> instructions on building Slicer from source are available here
> >>
> >>
> >>
> http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions#Building_the_latest_development_version
> >>
> >> Just FYI in case you would like to develop your tools within 3D Slicer.
> >>
> >> Andriy Fedorov
> >>
> >> > Thanks to both of you again,
> >> > john
> >> >
> >> > On Fri, Nov 13, 2009 at 11:20 AM, Bill Lorensen
> >> > <bill.lorensen at gmail.com>wrote:
> >> >
> >> >> John,
> >> >>
> >> >> The classes in Gaetan's paper now reside in the Insight/Code/Review.
> >> >>
> >> >> Bill
> >> >>
> >> >> On Fri, Nov 13, 2009 at 4:29 AM, John Drozd <john.drozd at gmail.com>
> >> >> wrote:
> >> >> > Thank you very much.  This is very helpful.
> >> >> >
> >> >> > john
> >> >> >
> >> >> > On Thu, Nov 12, 2009 at 3:42 PM, C.Cagatay Bilgin <
> bilgic at cs.rpi.edu>
> >> >> wrote:
> >> >> >>
> >> >> >> I use the following submission by Gaetan for
> >> >> >> that purpose. Note that It has way more
> >> >> >> morphological features than you asked for.
> >> >> >>
> >> >> >> http://www.insight-journal.org/browse/publication/176
> >> >> >>
> >> >> >> Regards,
> >> >> >>
> >> >> >>
> >> >>
> >> >>
> ----------------------------------------------------------------------------
> >> >> >> Cemal Cagatay Bilgin,
> >> >> >> Ph.D Candidate in Computer Science Department at RPI
> >> >> >> bilgic at cs.rpi.edu -
> >> >> >> http://www.cs.rpi.edu/~bilgic <http://www.cs.rpi.edu/%7Ebilgic><
> http://www.cs.rpi.edu/%7Ebilgic>
> >> >> >> Lally 01A, 110 8th Street Troy, NY 12180-3590, USA.
> >> >> >> Tel: (518) 276-8489, Fax:(518) 276-4033
> >> >> >>
> >> >> >> On Nov 12, 2009, at 12:31 PM, John Drozd wrote:
> >> >> >>
> >> >> >>> Hello,
> >> >> >>>
> >> >> >>> Using Examples/Segmentation/ConnectedThresholdImageFilter.cxx,
> >> >> >>> I successfully segmented ventricles from an mri image of a human
> >> >> >>> brain.
> >> >> >>>
> >> >> >>> Using ITK, I would like to calculate the statistical volume in
> mm^3
> >> >> >>> of
> >> >> >>> these segmented ventricles.
> >> >> >>> Are there any ITK functions that will allow me to calculate the
> >> >> >>> volume
> >> >> of
> >> >> >>> a segmented region?
> >> >> >>>
> >> >> >>> Thanks,
> >> >> >>> John
> >> >> >>> _____________________________________
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> >> >> >
> >> >> >
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> >> >> >
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