Can't find STAPLE filter in SimpleFilters

Support
1

Hi all,

The 3DSlicer wiki page for the Simple Filters Module lists a STAPLE Image Filter as one of the filter options. However I can’t seem to find it when using the software.

Can anyone help me locate it?

Thanks,
Katrina

2

It seems that it has been removed. Maybe @blowekamp knows more details.

3

Yes, Andras Lasso is correct it was removed. Here is the archived mailing thread about the discussion:
http://massmail.spl.harvard.edu/public-archives/slicer-devel/2016/041191.html

Could you please create an issue on the repository to fix this filter:

The documentation should also be updated. And this modules is in need of a bit of TLC.

4

Thanks Andras and Brad.

I’ve submitted the issue on github as suggested.

Kind regards,
Katrina

5

Are there any updates to this? I can see the STAPLE algorithm is still missing despite the github issue, and the mailing list link is down for me.

6

@lassoan @blowekamp @jcfr
I think I fixed one of the issues with the STAPLE filter by reading this discussion http://slicer-devel-archive.65872.n3.nabble.com/STAPLE-Filter-SimpleFilters-missing-V4-6-td4037712.html

However I am not sure how to validate if it is working? The algorithm accepts only one volume as input, and from my understanding it should accept multiple binary label maps and output a probability map. However the output is the same as the input. Any ideas?

7

How did you fix the issue? Which file have you modified?

8

For Slicer 4.10.2 in SimpleFilters.py, just above line 956 I inserted:
default = int( max( w.minimum, min(w.maximum, 50)))

And then reinserted the STAPLEImageFilter.json file that was deleted in an earlier commit.

9

If you only need to modify Python files then it is easy to test your modifications, as they take effect when you restart Slicer.

10

That’s not what I meant. I’ve already restarted Slicer and can see the STAPLE is available in Simple Filters.

However when I use it I can’t tell if it’s doing the correct processing. I expect it to produce a probability map as an output but instead it just spits out the input image as the output. If anyone has any experience using STAPLE in ITK I would appreciate their help!

11

Probably this question can be answered better on the ITK forum. If you post your question there, post the link here so that we can follow the discussion.