Slab reslicing

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Slab reslicing

San Jose Estepar, Raul,Ph.D.
Hi Slicer-devels


We have an application where we would like to have a slab reslicing view using a MIP or MinIP operator. Is there any option like this already available? I’ve been looking for it but I’ve not found anything.

If not, VTK already offers a vtkSlabReslicing class. So it should not be too complicated to include this feature that is quite common in other platforms like OsiriX.

What are the general thoughts about this feature?.  Could someone familiar with the SliceLogic code point us to parts of the code where this option could be incorporated?

Thanks a lot

Raul
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Re: Slab reslicing

lasso2
This feature is already available in Slicer, but we haven't added a user interface to configure it. You can enable it by a few lines of Python script as described here:

http://slicer-devel.65872.n3.nabble.com/Faster-slice-view-thick-slices-and-MIP-slice-view-mode-td4033264.html

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of San Jose Estepar, Raul,Ph.D.
Sent: November 7, 2015 4:27 PM
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Slab reslicing

Hi Slicer-devels


We have an application where we would like to have a slab reslicing view using a MIP or MinIP operator. Is there any option like this already available? I've been looking for it but I've not found anything.

If not, VTK already offers a vtkSlabReslicing class. So it should not be too complicated to include this feature that is quite common in other platforms like OsiriX.

What are the general thoughts about this feature?.  Could someone familiar with the SliceLogic code point us to parts of the code where this option could be incorporated?

Thanks a lot

Raul
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Re: Slab reslicing

San Jose Estepar, Raul,Ph.D.
In reply to this post by San Jose Estepar, Raul,Ph.D.
Hi Andras,

Thanks a lot. This is really helpful.

/R

> On Nov 7, 2015, at 5:05 PM, Andras Lasso <[hidden email]> wrote:
>
> This feature is already available in Slicer, but we haven't added a user interface to configure it. You can enable it by a few lines of Python script as described here:
>
> http://slicer-devel.65872.n3.nabble.com/Faster-slice-view-thick-slices-and-MIP-slice-view-mode-td4033264.html
>
> Andras
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of San Jose Estepar, Raul,Ph.D.
> Sent: November 7, 2015 4:27 PM
> To: SPL Slicer Devel <[hidden email]>
> Subject: [slicer-devel] Slab reslicing
>
> Hi Slicer-devels
>
>
> We have an application where we would like to have a slab reslicing view using a MIP or MinIP operator. Is there any option like this already available? I've been looking for it but I've not found anything.
>
> If not, VTK already offers a vtkSlabReslicing class. So it should not be too complicated to include this feature that is quite common in other platforms like OsiriX.
>
> What are the general thoughts about this feature?.  Could someone familiar with the SliceLogic code point us to parts of the code where this option could be incorporated?
>
> Thanks a lot
>
> Raul
> _______________________________________________
> slicer-devel mailing list
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> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>
>
> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
>

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Re: Slab reslicing

Jorge Onieva
Related with this thread, we were planning to show two windows and to compare
the "resliced" view and the original one at the same time. What do you think
it would be the best way to synchronize both views when the user navigates
through the scan?

Tx!

Jorge



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Re: Slab reslicing

Jorge Onieva
This post has NOT been accepted by the mailing list yet.
In reply to this post by San Jose Estepar, Raul,Ph.D.
Related with this thread, we were planning to show two windows and to compare the "resliced" view and the original one at the same time. What do you think it would be the best way to synchronize both views when the user navigates through the scan?

Tx!

Jorge
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Re: Slab reslicing

lasso2
In reply to this post by Jorge Onieva
The feature that you described is hot-link of slice views. Click and hold on the "link views" button to activate it.

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Jorge Onieva
Sent: Tuesday, November 10, 2015 12:54 PM
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] Slab reslicing

Related with this thread, we were planning to show two windows and to compare the "resliced" view and the original one at the same time. What do you think it would be the best way to synchronize both views when the user navigates through the scan?

Tx!

Jorge



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Re: Slab reslicing

Jorge Onieva
In reply to this post by Jorge Onieva
I didn't know that hot-link was able to do that. That's awesome, tx!

Jorge Onieva

On Tue, Nov 10, 2015 at 1:02 PM, Andras Lasso <[hidden email]> wrote:
The feature that you described is hot-link of slice views. Click and hold on the "link views" button to activate it.

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Jorge Onieva
Sent: Tuesday, November 10, 2015 12:54 PM
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] Slab reslicing

Related with this thread, we were planning to show two windows and to compare the "resliced" view and the original one at the same time. What do you think it would be the best way to synchronize both views when the user navigates through the scan?

Tx!

Jorge



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Re: Slab reslicing

mag
Hi,

I ran into this old post while trying to find out how to show MIP in the
slice viewers and was wondering how it would be possible to toggle between
the "resliced" and the original view in the same window (e.g. with a
button), instead of having two windows showing the "resliced" and original
view at the same time.

I'm showing MIP in the slice viewers with a button that execute this code
(from the script repository wiki page):

sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sliceLayerLogic = sliceLogic.GetBackgroundLayer()
reslice = sliceLayerLogic.GetReslice()
reslice.SetSlabModeToMax()
reslice.SetSlabNumberOfSlices(600)
reslice.SetSlabSliceSpacingFraction(0.5)
sliceNode.Modified()

But once I've changed to MIP I don't understand how to go back to the
original view.  I've tried to look into vtkImageReslice and
vtkImageSlabReslice but didn't find out how to do it (I'm still a beginner).
Is there an easy way to do it?

Thank you,

Marta




I didn't know that hot-link was able to do that. That's awesome, tx!

Jorge Onieva

On Tue, Nov 10, 2015 at 1:02 PM, Andras Lasso
&lt;lasso@&lt;mailto:lasso@&gt;> wrote:
The feature that you described is hot-link of slice views. Click and hold on
the "link views" button to activate it.

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers

Andras

-----Original Message-----
From:
slicer-devel-bounces@.harvard&lt;mailto:slicer-devel-bounces@.harvard&gt;
[mailto:slicer-devel-bounces@.harvard&lt;mailto:slicer-devel-bounces@.harvard&gt;]
On Behalf Of Jorge Onieva
Sent: Tuesday, November 10, 2015 12:54 PM
To: SPL Slicer Devel
&lt;slicer-devel@.harvard&lt;mailto:slicer-devel@.harvard&gt;>
Subject: Re: [slicer-devel] Slab reslicing

Related with this thread, we were planning to show two windows and to
compare the "resliced" view and the original one at the same time. What do
you think it would be the best way to synchronize both views when the user
navigates through the scan?

Tx!

Jorge





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View this message in context: http://slicer-devel.65872.n3.nabble.com/Slab-reslicing-tp4035510p4038168.html
Sent from the slicer-devel mailing list archive at Nabble.com.
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mag
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Re: Slab reslicing

mag
This post has NOT been accepted by the mailing list yet.
In reply to this post by Jorge Onieva
Hi,

I ran into this old post while trying to find out how to show MIP in the slice viewers and was wondering how it would be possible to toggle between the "resliced" and the original view in the same window (e.g. with a button), instead of having two windows showing the "resliced" and original view at the same time.

I'm showing MIP in the slice viewers with a button that execute this code (from the script repository wiki page):

sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sliceLayerLogic = sliceLogic.GetBackgroundLayer()
reslice = sliceLayerLogic.GetReslice()
reslice.SetSlabModeToMax()
reslice.SetSlabNumberOfSlices(600)
reslice.SetSlabSliceSpacingFraction(0.5)
sliceNode.Modified()

But once I've changed to MIP I don't understand how to go back to the original view.  I've tried to look into vtkImageReslice and vtkImageSlabReslice but didn't find out how to do it (I'm still a beginner).
Is there an easy way to do it?

Thank you,

Marta



<quote author="Jorge Onieva">
I didn't know that hot-link was able to do that. That's awesome, tx!

Jorge Onieva

On Tue, Nov 10, 2015 at 1:02 PM, Andras Lasso <[hidden email]<mailto:[hidden email]>> wrote:
The feature that you described is hot-link of slice views. Click and hold on the "link views" button to activate it.

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers

Andras

-----Original Message-----
From: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Jorge Onieva
Sent: Tuesday, November 10, 2015 12:54 PM
To: SPL Slicer Devel <[hidden email]<mailto:[hidden email]>>
Subject: Re: [slicer-devel] Slab reslicing

Related with this thread, we were planning to show two windows and to compare the "resliced" view and the original one at the same time. What do you think it would be the best way to synchronize both views when the user navigates through the scan?

Tx!

Jorge

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Re: Slab reslicing

lasso2
In reply to this post by mag

To disable thick slabs call: reslice.SetSlabNumberOfSlices(1)

 

Andras

 

From: [hidden email]
Sent: Friday, March 3, 2017 11:24 AM
To: [hidden email]
Subject: Re: [slicer-devel] Slab reslicing

 

Hi,

I ran into this old post while trying to find out how to show MIP in the
slice viewers and was wondering how it would be possible to toggle between
the "resliced" and the original view in the same window (e.g. with a
button), instead of having two windows showing the "resliced" and original
view at the same time.

I'm showing MIP in the slice viewers with a button that execute this code
(from the script repository wiki page):

sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sliceLayerLogic = sliceLogic.GetBackgroundLayer()
reslice = sliceLayerLogic.GetReslice()
reslice.SetSlabModeToMax()
reslice.SetSlabNumberOfSlices(600)
reslice.SetSlabSliceSpacingFraction(0.5)
sliceNode.Modified()

But once I've changed to MIP I don't understand how to go back to the
original view.  I've tried to look into vtkImageReslice and
vtkImageSlabReslice but didn't find out how to do it (I'm still a beginner).
Is there an easy way to do it?

Thank you,

Marta




I didn't know that hot-link was able to do that. That's awesome, tx!

Jorge Onieva

On Tue, Nov 10, 2015 at 1:02 PM, Andras Lasso
&lt;lasso@&lt;mailto:lasso@&gt;> wrote:
The feature that you described is hot-link of slice views. Click and hold on
the "link views" button to activate it.

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers

Andras

-----Original Message-----
From:
slicer-devel-bounces@.harvard&lt;mailto:slicer-devel-bounces@.harvard&gt;
[[hidden email]]
On Behalf Of Jorge Onieva
Sent: Tuesday, November 10, 2015 12:54 PM
To: SPL Slicer Devel
&lt;slicer-devel@.harvard&lt;mailto:slicer-devel@.harvard&gt;>
Subject: Re: [slicer-devel] Slab reslicing

Related with this thread, we were planning to show two windows and to
compare the "resliced" view and the original one at the same time. What do
you think it would be the best way to synchronize both views when the user
navigates through the scan?

Tx!

Jorge





--
View this message in context: http://slicer-devel.65872.n3.nabble.com/Slab-reslicing-tp4035510p4038168.html
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mag
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Re: Slab reslicing

mag
I had tried that and didn't work. I must have done something weird in my code
and I will find it, thank you.

I still have two things I don't understand about SlabReslice:

1) what is exactly the slabSliceSpacingFraction? My DICOM set has an axial
spacing of 0.3 mm and I want to view MIP over a slab of 20 mm, so I used:
nOfSlices = 20 / 0.3
reslice.SetSlabNumberOfSlicer(nOfSlices)

but what I should set slabSliceSpacingFraction equal to? I find the
explanation  here
<http://www.vtk.org/doc/nightly/html/classvtkImageReslice.html#adfcc3bd9a2f04a17e4328d437cb40947>  
a bit confusing:
"The slab spacing as a fraction of the output slice spacing.
When one of the various slab modes is chosen, each output slice is produced
by generating several "temporary" output slices and then combining them
according to the slab mode. By default, the spacing between these temporary
slices is the Z component of the OutputSpacing. This method sets the spacing
between these temporary slices to be a fraction of the output spacing."

2) (this is more of a general question) what I want in the end is to get the
values in the MIP projections in a numpy array and perform some calculations
on them. I found on a previous post how to get a numpy array from an
inputVolume.GetImageData() object, but how can I get imageData from the MIP
in the slice viewers?

Thank you again,

Marta



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Re: Slab reslicing

mag
This post has NOT been accepted by the mailing list yet.
In reply to this post by lasso2
I had tried that and didn't work. I must have done something weird in my code and I will find it, thank you.

I still have two things I don't understand about SlabReslice:

1) what is exactly the slabSliceSpacingFraction? My DICOM set has an axial spacing of 0.3 mm and I want to view MIP over a slab of 20 mm, so I used:
nOfSlices = 20 / 0.3
reslice.SetSlabNumberOfSlicer(nOfSlices)

but what I should set slabSliceSpacingFraction equal to? I find the explanation here a bit confusing:
"The slab spacing as a fraction of the output slice spacing.
When one of the various slab modes is chosen, each output slice is produced by generating several "temporary" output slices and then combining them according to the slab mode. By default, the spacing between these temporary slices is the Z component of the OutputSpacing. This method sets the spacing between these temporary slices to be a fraction of the output spacing."

2) (this is more of a general question) what I want in the end is to get the values in the MIP projections in a numpy array and perform some calculations on them. I found on a previous post how to get a numpy array from an inputVolume.GetImageData() object, but how can I get imageData from the MIP in the slice viewers?

Thank you again,

Marta
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Re: Slab reslicing

lasso2
In reply to this post by mag
Unfortunately, it is not easy to interpret those parameters - I didn't implement a GUI on Slicer to set the slab thickness because I did not have time to figure this out. Probably the best is to keep reading the documentation, source code of the filter, perform tests, maybe ask the filter's author - and once you've found how it works exactly, report back to us.

Andras

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of martag
Sent: March 3, 2017 15:00
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] Slab reslicing

I had tried that and didn't work. I must have done something weird in my code and I will find it, thank you.

I still have two things I don't understand about SlabReslice:

1) what is exactly the slabSliceSpacingFraction? My DICOM set has an axial spacing of 0.3 mm and I want to view MIP over a slab of 20 mm, so I used:
nOfSlices = 20 / 0.3
reslice.SetSlabNumberOfSlicer(nOfSlices)

but what I should set slabSliceSpacingFraction equal to? I find the explanation  here <http://www.vtk.org/doc/nightly/html/classvtkImageReslice.html#adfcc3bd9a2f04a17e4328d437cb40947>
a bit confusing:
"The slab spacing as a fraction of the output slice spacing.
When one of the various slab modes is chosen, each output slice is produced by generating several "temporary" output slices and then combining them according to the slab mode. By default, the spacing between these temporary slices is the Z component of the OutputSpacing. This method sets the spacing between these temporary slices to be a fraction of the output spacing."

2) (this is more of a general question) what I want in the end is to get the values in the MIP projections in a numpy array and perform some calculations on them. I found on a previous post how to get a numpy array from an
inputVolume.GetImageData() object, but how can I get imageData from the MIP in the slice viewers?

Thank you again,

Marta



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