[slicer-users] verifying dozens of registrations

Dominik Meier meier at bwh.harvard.edu
Mon Nov 8 12:12:36 EST 2010


Hi Steve

in terms of visualizations the suggestions from Greg & Isaiah are very good ones.

You could also consider subtraction images, if the two images registered have similar contrast. Edge misalignment shows up nicely in subtractions. Slicer module is called: "Subtract Images" (Filtering/Arithmetic)

A poor man's version of the scripting Isaiah mentioned would be to prep a set of commandline calls in a text editor and paste them in batch into a shell/executable window. To illustrate the concept, using image subtraction, a line would look like this:

/MyPathToSlicer/Slicer3  --launch /MyPathToSlicer/lib/Slicer3/Plugins/Subtract --order 1 image1.nrrd image2.nrrd subtractionresult.nrrd

you can then copy the above line and change the filenames accordingly and thus build subtraction (or checkerboard, if executable is avail.) images for all 60 sets in one go, and then just load and review.

For all modules you can find out what the commandline calls look like by opening the "Error Log" window, and replacing the Node info with corresponding input/output files.

For the checkerboard filter I could find only a .so file, no executable, but it may exist someplace other than the path above. 

Best,
Dominik


On Nov 8, 2010, at 10:25 AM, Gregory Sharp wrote:

> 
> Hi Steve,
> 
> To answer your original question, "no".  There is no interactive 
> keyhole or split-screen tool.  Isaiah's suggetion (color blending) 
> is the best available for interactive use.  
> 
> If you go that route, my further suggestion is to change compositing from
> "Alpha blend" to "Add", and change the lookup tables to "Warm shade" 
> and "Cool shade".  You may need to adjust window, level, and threshold.
> 
> -Greg
> 
> 
> On Mon, 8 Nov 2010 07:28:27 -0500
> Isaiah Norton <isaiah.norton at gmail.com> wrote:
> 
>> Hi Steve,
>> I usually use contrasting color palettes and the Fade button, ie orange and
>> green/blue (very common display in other programs).
>> 
>> The checkerboard filter is a CLI (command line interface) module, so if you
>> are comfortable with one of bash,batch,python,etc. the preparation of all
>> the comparison images could be scripted.
>> 
>> -Isaiah
>> 
>> On Sun, Nov 7, 2010 at 11:46 PM, Steve M. Robbins <steve at sumost.ca> wrote:
>> 
>>> Hi,
>>> 
>>> I'm presently using the "checkerboard" filter to verify registrations.
>>> It works OK, but I find it a little tedious to have to set up and run
>>> the filter each time.  Using the "fade between foreground/background"
>>> is easier to do in that it is ready to go once the two images have
>>> been loaded.  However, it is harder to judge that edges got matched
>>> satisfactorily.
>>> 
>>> Is there a plugin somewhere that displays the background with a small,
>>> moveable rectangle of the foreground?
>>> 
>>> Or another way to judge registrations when you have to look
>>> through 60 of them?
>>> 
>>> Thanks,
>>> -Steve
>>> 
>>> -----BEGIN PGP SIGNATURE-----
>>> Version: GnuPG v1.4.10 (GNU/Linux)
>>> 
>>> iD8DBQFM14Ch0i2bPSHbMcURAhqVAJ9JLLJE/1W/L4QLRGOzHLLBZKEV+gCeJ00l
>>> uRWvtUg7yh4o4jVG8Ptt+NI=
>>> =8gyz
>>> -----END PGP SIGNATURE-----
>>> 
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> 
> 
> -- 
> Greg Sharp, PhD
> Department of Radiation Oncology
> Massachusetts General Hospital
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