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Re: Measuring Volumes from MRI images

Posted by ToeKnee Lacey on Dec 02, 2005; 10:22am
URL: http://imagej.273.s1.nabble.com/Measuring-Volumes-from-MRI-images-tp3704319p3704323.html

Hi,

You might want to look at the <a href="http://ip.beckman.uiuc.edu/Software/SplineSnake/">

spline snake</a> plugin.

I've also developed some tools that we use to
manually markup cartilage knees from animal MRI data.  It's grown into quite
a sophisticated plugin allowing the user to identify the boundary over two
stacks simultaneously (pre and post treatment) whilst controlling the interations
between the two stacks to ensure that certain shape consistencies are enforced.


To get this going I had to overcome a couple of limitations with ImageJ.
 One was that it doesn't display images in their 'true' aspect ratio but instead
assumes pixels are square.  As we know this is often untrue in MRI.  The second
was the lack of subpixel mouse position information which is critical for
marking up small structures like these.  These I fixed by extending thes canvas
in imagej.  However this does require a Java 2 system.

I've also integrated
some code to communicate with an <a href="http://www.r-project.org/">R server</a>
so that imagej can squirt results directly to this excellent open source statistics
package either running locally or on a remote server (which can then do more
complex stats, generate webpage output etc).

I've developed some Matlab/Java
code to deserialise Java objects containing imagej structures for further
analysis in Matlab.  Matlab  runs a Java virtual machine so this is a relatively
simple process (once you fix the classloader!) and I find it another great
way to do further analysis on markups without all the bother of writing complex
file readers/writers or  compromising the design of your classes.  Again I
think this has generic utility.

Apologies for going off track a bit but
I'm interested to know if this stuff would be of wider utility.  Although
the specifics of the plugin are  geared towards our problem I think the framework
is a sound one and there are some bit here I haven't seen elsewhere.

-tony


--- ImageJ Interest Group <[hidden email] wrote:
Hi, I'm trying
to use ImageJ to get hippocampal volumes from structural MRI images.  I can
get them by tracing the HPC on each slice, using the measure function to get
area, exporting the data to excel and calculating volume from all of the areas,
but I'm wondering if anyone is doing this with a more sophisticated technique.
 I would appreciate any suggestions for specific plugins or tools that I might
be missing.  Thanks,
>
> Seth Shipman
>
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