Query re: volume or hand-drawn path lengths

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Query re: volume or hand-drawn path lengths

Sean Lisse
Slicers,

  Hello, I am a programmer and researcher working with Slicer 3D and the Pelvic Floor Research Group here at the University of Michigan.

  I have a problem that I've been working on regarding standardizing ways to measure pelvic anatomy (e.g. vaginal width, length, etc.) from our database of pelvic MRIs.  Using Slicer (3.6), I've worked out a workable system of basic linear 3D measurement between fiducials, but the problem becomes more complicated when attempting to measure curves.

  For instance, in order to measure anterior vaginal wall length, our current in-slicer solution is to draw a series of fiducials along the (curved) anterior wall, and then sum the straight-line distances between them.  We have more elegant solutions that involve exporting models from slicer into engineering software for analysis, but those are cumbersome to do in large batches.

  In my ideal world, I would be like able to use the editor (annotate) features to create a curved line in Slicer, have the system tell me path length in mm, and subdivide the curve (e.g. into five segments) to create fiducials from the subdivisions.  I'm currently thinking about creating a Slicer (3.6? 4?) module with the above capabilities, but don't want to duplicate existing features or create difficulty by "rolling my own" if there's a better way to solve the problem.

  I have spent some time exploring slicer 3 and slicer 4, including documentation, but the closest thing I've found to a curve with defined length is the ITK Path class, which at least could be a good starting point for module development.

  Any and all suggestions are welcome.

  Thank you for the time,
        Sean Lisse, OBGYN department, University of Michigan

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Re: Query re: volume or hand-drawn path lengths

Steve Pieper
Hi Sean - 

You're right, there's no module that does exactly what you describe.  The closest might be the Endoscopy module, which calculates a spline path along a series of fiducials:

If this looks close to what you need, you might be able to easily put in a calculation of the path length.

HTH,
Steve

On Wed, Aug 1, 2012 at 1:10 PM, Sean Lisse <[hidden email]> wrote:
Slicers,

  Hello, I am a programmer and researcher working with Slicer 3D and the Pelvic Floor Research Group here at the University of Michigan.

  I have a problem that I've been working on regarding standardizing ways to measure pelvic anatomy (e.g. vaginal width, length, etc.) from our database of pelvic MRIs.  Using Slicer (3.6), I've worked out a workable system of basic linear 3D measurement between fiducials, but the problem becomes more complicated when attempting to measure curves.

  For instance, in order to measure anterior vaginal wall length, our current in-slicer solution is to draw a series of fiducials along the (curved) anterior wall, and then sum the straight-line distances between them.  We have more elegant solutions that involve exporting models from slicer into engineering software for analysis, but those are cumbersome to do in large batches.

  In my ideal world, I would be like able to use the editor (annotate) features to create a curved line in Slicer, have the system tell me path length in mm, and subdivide the curve (e.g. into five segments) to create fiducials from the subdivisions.  I'm currently thinking about creating a Slicer (3.6? 4?) module with the above capabilities, but don't want to duplicate existing features or create difficulty by "rolling my own" if there's a better way to solve the problem.

  I have spent some time exploring slicer 3 and slicer 4, including documentation, but the closest thing I've found to a curve with defined length is the ITK Path class, which at least could be a good starting point for module development.

  Any and all suggestions are welcome.

  Thank you for the time,
        Sean Lisse, OBGYN department, University of Michigan

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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: Query re: volume or hand-drawn path lengths

madanrao
Hello,

One can use Slicer3 labelstatistics module to find volumes (mm 3 ). Lengths of each walls can be calculated from each volume by use of some standard readings you get from established solutions.

I hope this helps.

AM Mohan Rao

On Wed, Aug 1, 2012 at 11:39 PM, Steve Pieper <[hidden email]> wrote:
Hi Sean - 

You're right, there's no module that does exactly what you describe.  The closest might be the Endoscopy module, which calculates a spline path along a series of fiducials:

If this looks close to what you need, you might be able to easily put in a calculation of the path length.

HTH,
Steve

On Wed, Aug 1, 2012 at 1:10 PM, Sean Lisse <[hidden email]> wrote:
Slicers,

  Hello, I am a programmer and researcher working with Slicer 3D and the Pelvic Floor Research Group here at the University of Michigan.

  I have a problem that I've been working on regarding standardizing ways to measure pelvic anatomy (e.g. vaginal width, length, etc.) from our database of pelvic MRIs.  Using Slicer (3.6), I've worked out a workable system of basic linear 3D measurement between fiducials, but the problem becomes more complicated when attempting to measure curves.

  For instance, in order to measure anterior vaginal wall length, our current in-slicer solution is to draw a series of fiducials along the (curved) anterior wall, and then sum the straight-line distances between them.  We have more elegant solutions that involve exporting models from slicer into engineering software for analysis, but those are cumbersome to do in large batches.

  In my ideal world, I would be like able to use the editor (annotate) features to create a curved line in Slicer, have the system tell me path length in mm, and subdivide the curve (e.g. into five segments) to create fiducials from the subdivisions.  I'm currently thinking about creating a Slicer (3.6? 4?) module with the above capabilities, but don't want to duplicate existing features or create difficulty by "rolling my own" if there's a better way to solve the problem.

  I have spent some time exploring slicer 3 and slicer 4, including documentation, but the closest thing I've found to a curve with defined length is the ITK Path class, which at least could be a good starting point for module development.

  Any and all suggestions are welcome.

  Thank you for the time,
        Sean Lisse, OBGYN department, University of Michigan

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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