Fwd: Re: cut and paste behavior... volumetry

[roland makay]

--- Rasband Wayne <[hidden email]> wrote:

> You can paste into the same location in a different
> image by  
> restoring the Image (Edit>Selection>Restore
> Selection or shift-e)  
> before pasting.
>
> -wayne
>

Wayne, thanks a lot, it works...

A further question to the community: I am segmenting
organs on abdominal CT scans. After exporting the
segmented data to a new stack, I need to measure
volume. I tried the 'Measure Stack' plugin, which is
good because it takes slice spacing into account also.
For measurment, I have to select the ROI on the last
and first desired slice. Then it finds the
corresponding ROI-s on all slices. But it gets them
completely wrong, even if I treshold the images, so I
have to select ROI-s again on each slide again. It
also does not handle multiple ROI-s on a slice.
Voxel counter plugin does not give proper result
(probably does not take slice spacing in account).  
So does anybody have an idea for measuring volume on a
stack of Ct slices?

Thank you in advance,
Roland Makay


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[Wayne Rasband]

> A further question to the community: I am segmenting
> organs on abdominal CT scans. After exporting the
> segmented data to a new stack, I need to measure
> volume. I tried the 'Measure Stack' plugin, which is
> good because it takes slice spacing into account also.
> For measurment, I have to select the ROI on the last
> and first desired slice. Then it finds the
> corresponding ROI-s on all slices. But it gets them
> completely wrong, even if I treshold the images, so I
> have to select ROI-s again on each slide again. It
> also does not handle multiple ROI-s on a slice.
> Voxel counter plugin does not give proper result
> (probably does not take slice spacing in account).
> So does anybody have an idea for measuring
> volume on a stack of Ct slices?

There is an updated Voxel_Counter plugin at

     http://rsb.info.nih.gov/ij/plugins/voxel-counter.html

that does take the slice spacing into account.

-wayne

[Robert Dougherty]

Roland,

There may be a misunderstanding about Measure Stack's method filling in
intermediate ROIs.  It performs a geometrical interpolation to generate
ROIs on slices between slices that have user-drawn ROIs.  It does not
pay attention to the content of the image, so thresholding would not
have any effect on the ROI generation process.  The user is expected to
manually draw enough ROIs that interpolation works well.  Just drawing
ROIs on the first and last slice would only work for certain cone-like
volumes.

Bob


Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
[phone]
[hidden email]
http://www.optinav.com

>
> Wayne, thanks a lot, it works...
>
> A further question to the community: I am segmenting
> organs on abdominal CT scans. After exporting the
> segmented data to a new stack, I need to measure
> volume. I tried the 'Measure Stack' plugin, which is
> good because it takes slice spacing into account also.
> For measurment, I have to select the ROI on the last
> and first desired slice. Then it finds the
> corresponding ROI-s on all slices. But it gets them
> completely wrong, even if I treshold the images, so I
> have to select ROI-s again on each slide again. It
> also does not handle multiple ROI-s on a slice.
> Voxel counter plugin does not give proper result
> (probably does not take slice spacing in account).
> So does anybody have an idea for measuring volume on a
> stack of Ct slices?
>
> Thank you in advance,
> Roland Makay
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com