Interpolation of slices?

[Dominik Geisel]

Hello,

I am trying to do liver segmentation with ITK-SNAP and so far it seems like a perfect and accurate tool, except for one function I an unable to find and wonder if it's included at all.

Can ITK-SNAP interpolate between slices? For liver segmentation it would be really helpful, I use 0.625 mm slices and so the liver is around 300 slices, in most parts there is no drastic change from slice to slice.

Regards

Dominik

[Philip A Cook]

Hi,

Are you using the polygon tool to segment? You can copy and paste the polygon between slices.

If you want to resample the image, you can do that with c3d

http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Documentation

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[Dominik Geisel]

Copy/Paste is fine but still needs a lot of manual refining.

OsiriX has a feature called "Generate missing ROI" which just interpolates the slices in-between, that would be nice to have in ITK-SNAP

[Dorian Pustina]

Ahh,  I have been looking for that functionality but Snap doesn't  have it.  That would be a huge time saver.

[Solomon Tang]

There seems to be some advanced documentation on using C3D for this exact task, but it is unfinished. If anyone knows what the steps are in it's entirety, I'm sure many of us would love to know how it's done.

http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Advanced

[Paul Yushkevich]

Hello

I am happy to say that the very latest nightly builds of ITK-SNAP (for the last week) have this functionality available under "Tools->Interpolate Labels". 

It's pretty powerful, check it out!

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Shivali Dawda]

For some reason my version of ITK doesn't have the "draw over" function on interpolation?

Anyone else encounter this issue?

[Paul Yushkevich]

We simplified the GUI for interpolation in the more recent version (3.6). This was intentional. There is still a draw over control in the main control panel that can be used during label interpolation.

Thanks!
Paul

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[Akshay Goel]

Hello all, 

Can someone recommend the best interpolation settings for organ segmentation?

I see the default, use signed distance, and interpolate along single axis.

The source images are axial so the interpolation would likely be set to be across the axial direction. Curious about the other parameters?

On Thursday, June 1, 2017 at 7:14:44 AM UTC-4, Paul Yushkevich wrote:

We simplified the GUI for interpolation in the more recent version (3.6). This was intentional. There is still a draw over control in the main control panel that can be used during label interpolation.

Thanks!
Paul

On Thu, May 11, 2017 at 1:49 PM, Shivali Dawda <shival...@gmail.com> wrote:

For some reason my version of ITK doesn't have the "draw over" function on interpolation?

Anyone else encounter this issue?

On Wednesday, 15 June 2016 13:00:03 UTC+1, Dominik Geisel wrote:

Hello,

I am trying to do liver segmentation with ITK-SNAP and so far it seems like a perfect and accurate tool, except for one function I an unable to find and wonder if it's included at all.

Can ITK-SNAP interpolate between slices? For liver segmentation it would be really helpful, I use 0.625 mm slices and so the liver is around 300 slices, in most parts there is no drastic change from slice to slice.

Regards

Dominik

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