cutting planes not orthogonal

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cutting planes not orthogonal

Anka Kochanowska
Hi!
I am using Slicer 3.7 Alpha 1.0, but it was the same in 3.6.

I am loading a volume and displaying the cutting planes in 3D.
I apply some transformation to the volume.
Cutting planes are not more orthogonal and in 2D windows planes are displayed at an angle.
Everything is straighten when  I select Rotate to Volume plane in a small menu on one of 2D windows.
Then I reverse transform - in the data module drag volume out of transform. Again planes are not orthogonal, but now I cannot make them orthogonal, the previous trick does not work.
Using the reformat widget does not allow to do any precise positioning.

How do I reset the planes?

After applying transform fit to window does not work anymore.

Anka

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Re: [slicer-devel] cutting planes not orthogonal

Anka Kochanowska
Hi!
I think the alternative you talk about:

"An alternative (maybe not as general, but good enough) fix could be to change the “Rotate to Volume plane” to keep the slices orientations orthogonal if the slice viewers are linked.
"

is the solution, and not yet perfect.
When the user transforms a volume, he expects move and rotation of the whole as unity. Planes are the visual representation of the volume. The way it is done now gives the impression that cutting planes are independent of the volume. You need now 7 clicks to put the planes back together as they were before the transform! I am trying to find how Slicer could be used in operating room - a technician there has  no time for such tedious procedure.
Anka


On Thu, Jun 10, 2010 at 8:51 PM, Andras Lasso <[hidden email]> wrote:

Hi Anka,

 

Unfortunately, if you apply “Rotate to Volume” to any reformatted slice then it will rotate it to the same volume plane (to the plane that corresponds to the I axis of the image).

You can apply this workaround: Reset the three slice views to Axial, Sagittal, and Coronal orientations, and then apply “Rotate to Volume plane” on each slice view.

 

This behavior could be fixed by having separate slice orientation modes (“Background volume plane” and “Foreground volume plane”; or “Background volume I”, “Background volume J”, “Background volume K”, etc.) in addition to current Axial, Sagittal, Coronal, and Reformat modes (but it could make the GUI quite complex?). An alternative (maybe not as general, but good enough) fix could be to change the “Rotate to Volume plane” to keep the slices orientations orthogonal if the slice viewers are linked.

 

Andras

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Anka Kochanowska
Sent: Thursday, June 10, 2010 3:01 PM
To: [hidden email]; [hidden email]
Subject: [slicer-devel] cutting planes not orthogonal

 

Hi!
I am using Slicer 3.7 Alpha 1.0, but it was the same in 3.6.

I am loading a volume and displaying the cutting planes in 3D.
I apply some transformation to the volume.
Cutting planes are not more orthogonal and in 2D windows planes are displayed at an angle.
Everything is straighten when  I select Rotate to Volume plane in a small menu on one of 2D windows.
Then I reverse transform - in the data module drag volume out of transform. Again planes are not orthogonal, but now I cannot make them orthogonal, the previous trick does not work.
Using the reformat widget does not allow to do any precise positioning.

How do I reset the planes?

After applying transform fit to window does not work anymore.

Anka



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Re: [slicer-devel] cutting planes not orthogonal

pieper
Administrator
Hi Anka -

You might also consider using scene snapshots to store the views that
you will need to access during the procedure:

http://www.slicer.org/slicerWiki/index.php/Modules:SceneSnapshots-3.6

These store slice position, pan/zoom, visible volumes, models, etc.  You
can prepare these ahead of time and save it all in the mrml scene.  Then
it is only two clicks to get back to a known state.

HTH,
Steve



On Jun/15/10 9:18 PM, Andras Lasso wrote:

> Hi Anka,
>
> If you want to fix the displayed slice positions relative to the volume,
> then don't transform the volume (but transform all the other volumes,
> models, fiducials, etc. in the scene).
>
> If your problem is more complex or you need optimal user interface and
> behaviour for a specific application, then probably you have to develop
> your own interactive module for the procedure (this is done for most of
> the cases when Slicer is used in the OR).
>
> Andras
>
> *From:* [hidden email] [mailto:[hidden email]] *On Behalf Of *Anka
> Kochanowska
> *Sent:* June-15-10 3:14 PM
> *To:* Andras Lasso
> *Cc:* [hidden email]; [hidden email]
> *Subject:* Re: [slicer-devel] cutting planes not orthogonal
>
> Hi!
> I think the alternative you talk about:
>
> "An alternative (maybe not as general, but good enough) fix could be to
> change the “Rotate to Volume plane” to keep the slices orientations
> orthogonal if the slice viewers are linked."
>
> is the solution, and not yet perfect.
> When the user transforms a volume, he expects move and rotation of the
> whole as unity. Planes are the visual representation of the volume. The
> way it is done now gives the impression that cutting planes are
> independent of the volume. You need now 7 clicks to put the planes back
> together as they were before the transform! I am trying to find how
> Slicer could be used in operating room - a technician there has no time
> for such tedious procedure.
> Anka
>
> On Thu, Jun 10, 2010 at 8:51 PM, Andras Lasso <[hidden email]
> <mailto:[hidden email]>> wrote:
>
> Hi Anka,
>
> Unfortunately, if you apply “Rotate to Volume” to any reformatted slice
> then it will rotate it to the same volume plane (to the plane that
> corresponds to the I axis of the image).
>
> You can apply this workaround: Reset the three slice views to Axial,
> Sagittal, and Coronal orientations, and then apply “Rotate to Volume
> plane” on each slice view.
>
> This behavior could be fixed by having separate slice orientation modes
> (“Background volume plane” and “Foreground volume plane”; or “Background
> volume I”, “Background volume J”, “Background volume K”, etc.) in
> addition to current Axial, Sagittal, Coronal, and Reformat modes (but it
> could make the GUI quite complex?). An alternative (maybe not as
> general, but good enough) fix could be to change the “Rotate to Volume
> plane” to keep the slices orientations orthogonal if the slice viewers
> are linked.
>
> Andras
>
> *From:* [hidden email]
> <mailto:[hidden email]>
> [mailto:[hidden email]
> <mailto:[hidden email]>] *On Behalf Of *Anka
> Kochanowska
> *Sent:* Thursday, June 10, 2010 3:01 PM
> *To:* [hidden email]
> <mailto:[hidden email]>; [hidden email]
> <mailto:[hidden email]>
> *Subject:* [slicer-devel] cutting planes not orthogonal
>
> Hi!
> I am using Slicer 3.7 Alpha 1.0, but it was the same in 3.6.
>
> I am loading a volume and displaying the cutting planes in 3D.
> I apply some transformation to the volume.
> Cutting planes are not more orthogonal and in 2D windows planes are
> displayed at an angle.
> Everything is straighten when I select Rotate to Volume plane in a small
> menu on one of 2D windows.
> Then I reverse transform - in the data module drag volume out of
> transform. Again planes are not orthogonal, but now I cannot make them
> orthogonal, the previous trick does not work.
> Using the reformat widget does not allow to do any precise positioning.
>
> How do I reset the planes?
>
> After applying transform fit to window does not work anymore.
>
> Anka
>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject