Re: Real-time transform visualization in the Slicer core

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Re: Real-time transform visualization in the Slicer core

Andras Lasso-2

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


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Re: Real-time transform visualization in the Slicer core

Dominik Meier
Very cool and extremely useful ! Many thanks !
-- Dominik


On Apr 17, 2014, at 12:55 PM, Andras Lasso <[hidden email]> wrote:

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.
 
Demo video:
 
Documentation, screenshots:
 
Andras
 
From: Andras Lasso 
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core
 
Hi all,
 
We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.
 
We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.
 
A short video demonstrating the main features:
 
Windows installer, test data, screenshots:
 
Source code:
 
The following features are ready:
·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform
·         Transform information displayed in the Transforms module (type of transform, basic properties)
·         Transform visualization:
o   Built into the Transforms module
o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)
o   All transform types are supported (chains of transforms as well)
o   Visualization in the slice viewers
o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)
o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)
o   Built-in colormap editor
·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform
 
Thanks in advance.
Andras
 
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Re: Real-time transform visualization in the Slicer core

Murat Maga
In reply to this post by Andras Lasso-2

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Real-time transform visualization in the Slicer

Murat Maga
In reply to this post by Andras Lasso-2

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Real-time transform visualization in the Slicer core

Andras Lasso-2
In reply to this post by Murat Maga

Hi Murat,

 

The Units module supposed to address these kinds of problems. For example, you could set micron as length unit  and then all the length values would be treated as microns. To make this work well, the units module would probably need some fixes and improvements:

1.       The unit-aware widgets are not very stable yet (I’ve tried to use them but caused difficult-to-debug crashes, so I gave up).

2.       Probably need to specify a scaling value in addition to the unit name. For example, if we have 100x smaller images than typical human images then we should set 10.0 micron as length unit (and not just use micron as unit, because then all of the length values would be 10x larger, which is almost as bad as having all length values 100x smaller).

Maybe you should discuss about your needs with Julien Finet, if he can implement these improvements then it should be no problem to make the slider limit values adjustable.

 

In the short term I would suggest to scale your data manually, e.g., if your data sets are typically 100x smaller than human data sets then simply apply a 100x scaling after you import your data. Alternatively, you can set any value in the transform display node from Python.

 

Andras

 

From: Murat Maga [mailto:[hidden email]]
Sent: Thursday, April 17, 2014 1:13 PM
To: Andras Lasso; [hidden email]; 'Slicer Developers Mailing List'
Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

 

From: [hidden email] [[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/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
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Re: Real-time transform visualization in the Slicer core

Murat Maga

HI Andras,

 

If you are referring to Units tab under the applications setting, I can definitely say that it doesn’t do anything for me. It does report the values in ums under the volume module, but when I switch to linear transform and use the slider for translations the increments of 1 is certainly not in microns, but in millimeters.

 

Or if I put a ruler, then the scales of text or ticks so off, that I can’t even modify them via the controls provided (and some of them don’t let you type in small decimals).

 

M

 

 

From: Andras Lasso [mailto:[hidden email]]
Sent: Thursday, April 17, 2014 11:18 AM
To: Murat Maga; [hidden email]; 'Slicer Developers Mailing List'
Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Murat,

 

The Units module supposed to address these kinds of problems. For example, you could set micron as length unit  and then all the length values would be treated as microns. To make this work well, the units module would probably need some fixes and improvements:

1.       The unit-aware widgets are not very stable yet (I’ve tried to use them but caused difficult-to-debug crashes, so I gave up).

2.       Probably need to specify a scaling value in addition to the unit name. For example, if we have 100x smaller images than typical human images then we should set 10.0 micron as length unit (and not just use micron as unit, because then all of the length values would be 10x larger, which is almost as bad as having all length values 100x smaller).

Maybe you should discuss about your needs with Julien Finet, if he can implement these improvements then it should be no problem to make the slider limit values adjustable.

 

In the short term I would suggest to scale your data manually, e.g., if your data sets are typically 100x smaller than human data sets then simply apply a 100x scaling after you import your data. Alternatively, you can set any value in the transform display node from Python.

 

Andras

 

From: Murat Maga [[hidden email]]
Sent: Thursday, April 17, 2014 1:13 PM
To: Andras Lasso; [hidden email]; 'Slicer Developers Mailing List'
Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

 

From: [hidden email] [[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/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
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Re: Real-time transform visualization in the Slicer core

Julien Finet
Hi Murat, 

Can you please write some bug reports [1] with detailed workflow and ideally with dataset to reproduce the issues.


Thanks,
Julien. 


On Thu, Apr 17, 2014 at 2:49 PM, Murat Maga <[hidden email]> wrote:

HI Andras,

 

If you are referring to Units tab under the applications setting, I can definitely say that it doesn’t do anything for me. It does report the values in ums under the volume module, but when I switch to linear transform and use the slider for translations the increments of 1 is certainly not in microns, but in millimeters.

 

Or if I put a ruler, then the scales of text or ticks so off, that I can’t even modify them via the controls provided (and some of them don’t let you type in small decimals).

 

M

 

 

From: Andras Lasso [mailto:[hidden email]]
Sent: Thursday, April 17, 2014 11:18 AM
To: Murat Maga; [hidden email]; 'Slicer Developers Mailing List'


Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Murat,

 

The Units module supposed to address these kinds of problems. For example, you could set micron as length unit  and then all the length values would be treated as microns. To make this work well, the units module would probably need some fixes and improvements:

1.       The unit-aware widgets are not very stable yet (I’ve tried to use them but caused difficult-to-debug crashes, so I gave up).

2.       Probably need to specify a scaling value in addition to the unit name. For example, if we have 100x smaller images than typical human images then we should set 10.0 micron as length unit (and not just use micron as unit, because then all of the length values would be 10x larger, which is almost as bad as having all length values 100x smaller).

Maybe you should discuss about your needs with Julien Finet, if he can implement these improvements then it should be no problem to make the slider limit values adjustable.

 

In the short term I would suggest to scale your data manually, e.g., if your data sets are typically 100x smaller than human data sets then simply apply a 100x scaling after you import your data. Alternatively, you can set any value in the transform display node from Python.

 

Andras

 

From: Murat Maga [[hidden email]]
Sent: Thursday, April 17, 2014 1:13 PM
To: Andras Lasso; [hidden email]; 'Slicer Developers Mailing List'
Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

 

From: [hidden email] [[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


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Re: Real-time transform visualization in the Slicer core

Andras Lasso-2

Note that if you change the unit from millimeter to micron then you have to apply 1000x scaling to your data (just create a linear transform, fill the diagonal with [1000, 1000, 1000, 1], and apply it to all your data nodes).

 

Andras

 

From: Julien Finet [mailto:[hidden email]]
Sent: Thursday, April 17, 2014 2:53 PM
To: Murat Maga
Cc: Andras Lasso; [hidden email]
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Murat, 

 

Can you please write some bug reports [1] with detailed workflow and ideally with dataset to reproduce the issues.

 

 

Thanks,

Julien. 

 

On Thu, Apr 17, 2014 at 2:49 PM, Murat Maga <[hidden email]> wrote:

HI Andras,

 

If you are referring to Units tab under the applications setting, I can definitely say that it doesn’t do anything for me. It does report the values in ums under the volume module, but when I switch to linear transform and use the slider for translations the increments of 1 is certainly not in microns, but in millimeters.

 

Or if I put a ruler, then the scales of text or ticks so off, that I can’t even modify them via the controls provided (and some of them don’t let you type in small decimals).

 

M

 

 

From: Andras Lasso [mailto:[hidden email]]
Sent: Thursday, April 17, 2014 11:18 AM
To: Murat Maga; [hidden email]; 'Slicer Developers Mailing List'


Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Murat,

 

The Units module supposed to address these kinds of problems. For example, you could set micron as length unit  and then all the length values would be treated as microns. To make this work well, the units module would probably need some fixes and improvements:

1.       The unit-aware widgets are not very stable yet (I’ve tried to use them but caused difficult-to-debug crashes, so I gave up).

2.       Probably need to specify a scaling value in addition to the unit name. For example, if we have 100x smaller images than typical human images then we should set 10.0 micron as length unit (and not just use micron as unit, because then all of the length values would be 10x larger, which is almost as bad as having all length values 100x smaller).

Maybe you should discuss about your needs with Julien Finet, if he can implement these improvements then it should be no problem to make the slider limit values adjustable.

 

In the short term I would suggest to scale your data manually, e.g., if your data sets are typically 100x smaller than human data sets then simply apply a 100x scaling after you import your data. Alternatively, you can set any value in the transform display node from Python.

 

Andras

 

From: Murat Maga [[hidden email]]
Sent: Thursday, April 17, 2014 1:13 PM
To: Andras Lasso; [hidden email]; 'Slicer Developers Mailing List'
Subject: RE: [slicer-users] Real-time transform visualization in the Slicer core

 

Hi Andras,

 

Looks great. I see from demo that the spacing is always in mm’s. I work with samples about 5mm in diameter with resolutions from 10-35 microns. One of the overall challenges using Slicer for small animal imaging (especially for fetal samples) is that everything renders so small. So I don’t know if your spacing accepts an input like 0.010 mm (most such variables in Slicer don’t). Otherwise I will probably end up with about 2 vectors. So adjusting the unit or being able to enter small decimal values would be my request.

 

Thanks,

Murat

 

 

 

 

 

From: [hidden email] [[hidden email]] On Behalf Of Andras Lasso
Sent: Thursday, April 17, 2014 9:55 AM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Re: [slicer-users] Real-time transform visualization in the Slicer core

 

FYI, the transform display feature is now available in the Slicer nightly builds. Any feedback is welcome.

 

Demo video:

http://youtu.be/kZUAfR0mqqI?hd=1

 

Documentation, screenshots:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

 

Andras

 

From: Andras Lasso
Sent: Friday, April 04, 2014 4:32 PM
To: '[hidden email]'; 'Slicer Developers Mailing List ([hidden email])'
Subject: Real-time transform visualization in the Slicer core

 

Hi all,

 

We would like to collect some feedback on a feature that is planned to be integrated into the Slicer core soon.

 

We’ve further extended non-linear transform support and implemented real-time transform visualization by reworking and optimizing the TransformVisualizer extension. Please have a look at the video/screenshots or try it yourself (an installer package is available for Win64, the source code is on github) and let us know if you have any comments.

 

A short video demonstrating the main features:

http://screencast.com/t/Z6dQVjK3m

 

Windows installer, test data, screenshots:

http://1drv.ms/1fSVcBU

 

Source code:

https://github.com/lassoan/Slicer/tree/TransformDisplayableManager

 

The following features are ready:

·         Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform

·         Transform information displayed in the Transforms module (type of transform, basic properties)

·         Transform visualization:

o   Built into the Transforms module

o   Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)

o   All transform types are supported (chains of transforms as well)

o   Visualization in the slice viewers

o   Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)

o   Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)

o   Built-in colormap editor

·         MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform

 

Thanks in advance.

Andras

 


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Re: Real-time transform visualization in the Slicer core

Kikinis, Ron,M.D.
BTW:
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Units

On 4/17/14, 12:00 PM, Andras Lasso wrote:

> Note that if you change the unit from millimeter to micron then you have
> to apply 1000x scaling to your data (just create a linear transform,
> fill the diagonal with [1000, 1000, 1000, 1], and apply it to all your
> data nodes).
>
> Andras
>
> *From:*Julien Finet [mailto:[hidden email]]
> *Sent:* Thursday, April 17, 2014 2:53 PM
> *To:* Murat Maga
> *Cc:* Andras Lasso; [hidden email]
> *Subject:* Re: [slicer-users] Real-time transform visualization in the
> Slicer core
>
> Hi Murat,
>
> Can you please write some bug reports [1] with detailed workflow and
> ideally with dataset to reproduce the issues.
>
> [1]: http://www.na-mic.org/Bug/view_all_bug_page.php
>
> Thanks,
>
> Julien.
>
> On Thu, Apr 17, 2014 at 2:49 PM, Murat Maga <[hidden email]
> <mailto:[hidden email]>> wrote:
>
> HI Andras,
>
> If you are referring to Units tab under the applications setting, I can
> definitely say that it doesn’t do anything for me. It does report the
> values in ums under the volume module, but when I switch to linear
> transform and use the slider for translations the increments of 1 is
> certainly not in microns, but in millimeters.
>
> Or if I put a ruler, then the scales of text or ticks so off, that I
> can’t even modify them via the controls provided (and some of them don’t
> let you type in small decimals).
>
> M
>
> *From:*Andras Lasso [mailto:[hidden email] <mailto:[hidden email]>]
> *Sent:* Thursday, April 17, 2014 11:18 AM
> *To:* Murat Maga; [hidden email]
> <mailto:[hidden email]>; 'Slicer Developers Mailing List'
>
>
> *Subject:* RE: [slicer-users] Real-time transform visualization in the
> Slicer core
>
> Hi Murat,
>
> The Units module supposed to address these kinds of problems. For
> example, you could set micron as length unit  and then all the length
> values would be treated as microns. To make this work well, the units
> module would probably need some fixes and improvements:
>
> 1.The unit-aware widgets are not very stable yet (I’ve tried to use them
> but caused difficult-to-debug crashes, so I gave up).
>
> 2.Probably need to specify a scaling value in addition to the unit name.
> For example, if we have 100x smaller images than typical human images
> then we should set 10.0 micron as length unit (and not just use micron
> as unit, because then all of the length values would be 10x larger,
> which is almost as bad as having all length values 100x smaller).
>
> Maybe you should discuss about your needs with Julien Finet, if he can
> implement these improvements then it should be no problem to make the
> slider limit values adjustable.
>
> In the short term I would suggest to scale your data manually, e.g., if
> your data sets are typically 100x smaller than human data sets then
> simply apply a 100x scaling after you import your data. Alternatively,
> you can set any value in the transform display node from Python.
>
> Andras
>
> *From:*Murat Maga [mailto:[hidden email]]
> *Sent:* Thursday, April 17, 2014 1:13 PM
> *To:* Andras Lasso; [hidden email]
> <mailto:[hidden email]>; 'Slicer Developers Mailing List'
> *Subject:* RE: [slicer-users] Real-time transform visualization in the
> Slicer core
>
> Hi Andras,
>
> Looks great. I see from demo that the spacing is always in mm’s. I work
> with samples about 5mm in diameter with resolutions from 10-35 microns.
> One of the overall challenges using Slicer for small animal imaging
> (especially for fetal samples) is that everything renders so small. So I
> don’t know if your spacing accepts an input like 0.010 mm (most such
> variables in Slicer don’t). Otherwise I will probably end up with about
> 2 vectors. So adjusting the unit or being able to enter small decimal
> values would be my request.
>
> Thanks,
>
> Murat
>
> *From:*[hidden email]
> <mailto:[hidden email]>
> [mailto:[hidden email]] *On Behalf Of *Andras Lasso
> *Sent:* Thursday, April 17, 2014 9:55 AM
> *To:* '[hidden email]
> <mailto:[hidden email]>'; 'Slicer Developers Mailing List
> ([hidden email] <mailto:[hidden email]>)'
> *Subject:* Re: [slicer-users] Real-time transform visualization in the
> Slicer core
>
> FYI, the transform display feature is now available in the Slicer
> nightly builds. Any feedback is welcome.
>
> Demo video:
>
> http://youtu.be/kZUAfR0mqqI?hd=1
>
> Documentation, screenshots:
>
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms
>
> Andras
>
> *From:*Andras Lasso
> *Sent:* Friday, April 04, 2014 4:32 PM
> *To:* '[hidden email]
> <mailto:[hidden email]>'; 'Slicer Developers Mailing List
> ([hidden email] <mailto:[hidden email]>)'
> *Subject:* Real-time transform visualization in the Slicer core
>
> Hi all,
>
> We would like to collect some feedback on a feature that is planned to
> be integrated into the Slicer core soon.
>
> We’ve further extended non-linear transform support and implemented
> real-time transform visualization by reworking and optimizing the
> TransformVisualizer extension. Please have a look at the
> video/screenshots or try it yourself (an installer package is available
> for Win64, the source code is on github) and let us know if you have any
> comments.
>
> A short video demonstrating the main features:
>
> http://screencast.com/t/Z6dQVjK3m
>
> Windows installer, test data, screenshots:
>
> http://1drv.ms/1fSVcBU
>
> Source code:
>
> https://github.com/lassoan/Slicer/tree/TransformDisplayableManager
>
> The following features are ready:
>
> ·Support non-linear transforms in the Transforms module: allow Apply,
> Harden, Invert transform
>
> ·Transform information displayed in the Transforms module (type of
> transform, basic properties)
>
> ·Transform visualization:
>
> oBuilt into the Transforms module
>
> oThree main modes: Glyphs (show an array of arrows, cones, spheres),
> Grid (show a deformed grid), or Contour (show isolines/isosurfaces for
> specified displacement magnitude values)
>
> oAll transform types are supported (chains of transforms as well)
>
> oVisualization in the slice viewers
>
> oVisualization in the 3D viewers, in the specified region (region can be
> a slice viewer, a volume, or a ROI widget)
>
> oReal-time update: if the transform (or any visualization parameter) is
> changed then the visualization is updated immediately (interactive
> visualization while editing the transform)
>
> oBuilt-in colormap editor
>
> ·MetaImage (mha), NIFTI (nii) vector volumes can be loaded as
> displacement field (grid) transform
>
> Thanks in advance.
>
> Andras
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email] <mailto:[hidden email]>
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to
> [hidden email]
> <mailto:[hidden email]> with unsubscribe
> as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/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.
>
>
>
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
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