verifying dozens of registrations

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verifying dozens of registrations

Steve M. Robbins
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

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Re: verifying dozens of registrations

inorton
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 <[hidden email]> 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

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Re: verifying dozens of registrations

Sharp, Gregory C.

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 <[hidden email]> 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 <[hidden email]> 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-----
> >
> > _______________________________________________
> > 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
> >


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
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Re: verifying dozens of registrations

Marco Ruiz
In reply to this post by Steve M. Robbins
Hi Greg, Steve,

Just as an FYI, NAMIC has a system to execute parameter explorations called "GWE" (Grid Wizard Enterprise). You can find more about it at: http://www.gridwizardenterprise.org/. Also this system has a companion tool called "RSE" (Record Set Explorer which allows you to navigate any type of record sets: parameters used for parameter exploration experiments as well as their results sets generated by executing them using GWE.

These are 2 short YouTube videos demoing their usage:

If you are interested, I can walk you through the setup and usage of the system in your own machines which can take up to 10 minutes and in clusters you may have access on which may take a little longer depending on the particulars of its environment.

Marco.


-------- Original Message --------
Subject: Re: [slicer-users] verifying dozens of registrations
Date: Mon, 8 Nov 2010 10:25:00 -0500
From: Gregory Sharp <[hidden email]>
To: [hidden email]


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 <[hidden email]> 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 <[hidden email]> 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-----
>
> _______________________________________________
> 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
>


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject



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Re: verifying dozens of registrations

Dominik Meier
In reply to this post by Sharp, Gregory C.
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 <[hidden email]> 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 <[hidden email]> 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

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Version: GnuPG v1.4.10 (GNU/Linux)

iD8DBQFM14Ch0i2bPSHbMcURAhqVAJ9JLLJE/1W/L4QLRGOzHLLBZKEV+gCeJ00l
uRWvtUg7yh4o4jVG8Ptt+NI=
=8gyz
-----END PGP SIGNATURE-----

_______________________________________________
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



--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
_______________________________________________
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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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