Label Map Smoothing and Surface Toolbox tutorials

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Label Map Smoothing and Surface Toolbox tutorials

Gonzalo Rojas Costa
Hi:

  Where I can find "Label Map Smoothing" and "Surface Toolbox" more
detailed tutorials than the one that appears in
http://www.slicer.org/slicerWiki/index.php/Modules:PythonSurfaceToolbox-Documentation-3.6
?

  Sincerely,


Gonzalo Rojas Costa
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Re: Label Map Smoothing and Surface Toolbox tutorials

Steve Pieper
Hi Gonzalo -

That's all there is on those topics right now in terms of documentation.  But if you have questions let us know.

Best,
Steve

On Mon, Sep 19, 2011 at 8:42 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi:

 Where I can find "Label Map Smoothing" and "Surface Toolbox" more
detailed tutorials than the one that appears in
http://www.slicer.org/slicerWiki/index.php/Modules:PythonSurfaceToolbox-Documentation-3.6
?

 Sincerely,


Gonzalo Rojas Costa
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Re: Label Map Smoothing and Surface Toolbox tutorials

Gonzalo Rojas Costa
Hi Steve:

  I have the following questions about Surface Models related modules:

I) Label Map Smoothing module: that module smooths a specified label
in a label map to get a better surface model ?
II) Surface Toolbox module:
a) Surface Decimation --> Boundary vertex deletion: what it means ?
b) Surface Smoothing --> Which is the difference between Laplace and
Taubin surface smoothing algorithms ?
c) Surface Normals: a more detailed explanation of each parameter ?

  Sincerely,


Gonzalo Rojas Costa


On Tue, Sep 20, 2011 at 2:08 PM, Steve Pieper <[hidden email]> wrote:
> Hi Gonzalo -
>
> That's all there is on those topics right now in terms of documentation.
> But if you have questions let us know.
>
> Best,
> Steve
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Re: Label Map Smoothing and Surface Toolbox tutorials

Steve Pieper

Hi Gonzalo -


On Tue, Sep 20, 2011 at 11:45 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi Steve:

 I have the following questions about Surface Models related modules:

I) Label Map Smoothing module: that module smooths a specified label
in a label map to get a better surface model ?

That module was contributed by our colleagues in Utah based on a similar tool in the scirun package, so you might find some more information from their site (try google).  In general yes, the goal is to clean up ridges in the label volume to get a better model.
 
II) Surface Toolbox module:
a) Surface Decimation --> Boundary vertex deletion: what it means ? 
b) Surface Smoothing --> Which is the difference between Laplace and
Taubin surface smoothing algorithms ?
c) Surface Normals: a more detailed explanation of each parameter ?

Ah, yes, well I guess there is more detailed info available on those topics - they refer to parameters of the underlying VTK filters which are described here:

http://www.vtk.org/doc/nightly/html/classvtkDecimatePro.html#details

http://www.vtk.org/doc/nightly/html/classvtkSmoothPolyDataFilter.html

http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details

http://www.vtk.org/doc/nightly/html/classvtkPolyDataNormals.html#details

I added these links to the references section of the documentation wiki page.

Thanks for the good questions!
-Steve


 Sincerely,


Gonzalo Rojas Costa


On Tue, Sep 20, 2011 at 2:08 PM, Steve Pieper <[hidden email]> wrote:
> Hi Gonzalo -
>
> That's all there is on those topics right now in terms of documentation.
> But if you have questions let us know.
>
> Best,
> Steve


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Re: Label Map Smoothing and Surface Toolbox tutorials

Gonzalo Rojas Costa
Hi Steve:

  I tested the surface decimation function of  Surface Toolbox module
with some different mesh and different options/values of the function,
but I didn't got any resulting mesh... Why ?...

  Sincerely,


Gonzalo Rojas Costa


On Wed, Sep 21, 2011 at 11:33 AM, Steve Pieper <[hidden email]> wrote:

>
> Hi Gonzalo -
>
>
> On Tue, Sep 20, 2011 at 11:45 PM, Gonzalo Rojas Costa
> <[hidden email]> wrote:
>>
>> Hi Steve:
>>
>>  I have the following questions about Surface Models related modules:
>>
>> I) Label Map Smoothing module: that module smooths a specified label
>> in a label map to get a better surface model ?
>
> That module was contributed by our colleagues in Utah based on a similar
> tool in the scirun package, so you might find some more information from
> their site (try google).  In general yes, the goal is to clean up ridges in
> the label volume to get a better model.
>
>>
>> II) Surface Toolbox module:
>> a) Surface Decimation --> Boundary vertex deletion: what it means ?
>>
>> b) Surface Smoothing --> Which is the difference between Laplace and
>> Taubin surface smoothing algorithms ?
>> c) Surface Normals: a more detailed explanation of each parameter ?
>
> Ah, yes, well I guess there is more detailed info available on those topics
> - they refer to parameters of the underlying VTK filters which are described
> here:
>
> http://www.vtk.org/doc/nightly/html/classvtkDecimatePro.html#details
>
> http://www.vtk.org/doc/nightly/html/classvtkSmoothPolyDataFilter.html
>
> http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details
>
> http://www.vtk.org/doc/nightly/html/classvtkPolyDataNormals.html#details
>
> I added these links to the references section of the documentation wiki
> page.
>
> Thanks for the good questions!
> -Steve
>
>>
>>  Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>> On Tue, Sep 20, 2011 at 2:08 PM, Steve Pieper <[hidden email]> wrote:
>> > Hi Gonzalo -
>> >
>> > That's all there is on those topics right now in terms of documentation.
>> > But if you have questions let us know.
>> >
>> > Best,
>> > Steve
>
>
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Re: Label Map Smoothing and Surface Toolbox tutorials

Steve Pieper
Hi Gonzalo -

Which version of slicer are you using?  I just tried with the current release (3.6.3 on window 32bit) and all worked as expected.

-Steve

On Wed, Sep 21, 2011 at 10:28 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi Steve:

 I tested the surface decimation function of  Surface Toolbox module
with some different mesh and different options/values of the function,
but I didn't got any resulting mesh... Why ?...

 Sincerely,


Gonzalo Rojas Costa


On Wed, Sep 21, 2011 at 11:33 AM, Steve Pieper <[hidden email]> wrote:
>
> Hi Gonzalo -
>
>
> On Tue, Sep 20, 2011 at 11:45 PM, Gonzalo Rojas Costa
> <[hidden email]> wrote:
>>
>> Hi Steve:
>>
>>  I have the following questions about Surface Models related modules:
>>
>> I) Label Map Smoothing module: that module smooths a specified label
>> in a label map to get a better surface model ?
>
> That module was contributed by our colleagues in Utah based on a similar
> tool in the scirun package, so you might find some more information from
> their site (try google).  In general yes, the goal is to clean up ridges in
> the label volume to get a better model.
>
>>
>> II) Surface Toolbox module:
>> a) Surface Decimation --> Boundary vertex deletion: what it means ?
>>
>> b) Surface Smoothing --> Which is the difference between Laplace and
>> Taubin surface smoothing algorithms ?
>> c) Surface Normals: a more detailed explanation of each parameter ?
>
> Ah, yes, well I guess there is more detailed info available on those topics
> - they refer to parameters of the underlying VTK filters which are described
> here:
>
> http://www.vtk.org/doc/nightly/html/classvtkDecimatePro.html#details
>
> http://www.vtk.org/doc/nightly/html/classvtkSmoothPolyDataFilter.html
>
> http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details
>
> http://www.vtk.org/doc/nightly/html/classvtkPolyDataNormals.html#details
>
> I added these links to the references section of the documentation wiki
> page.
>
> Thanks for the good questions!
> -Steve
>
>>
>>  Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>> On Tue, Sep 20, 2011 at 2:08 PM, Steve Pieper <[hidden email]> wrote:
>> > Hi Gonzalo -
>> >
>> > That's all there is on those topics right now in terms of documentation.
>> > But if you have questions let us know.
>> >
>> > Best,
>> > Steve
>
>


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Re: Label Map Smoothing and Surface Toolbox tutorials

Steve Pieper
Ahh - interesting!  I think you found something we'd overlooked - the model maker turns the triangles into triangle strips for faster rendering, but the surface toolbox assumes things will be independent triangles.

Turns out it was a simple thing to add the functionality so I went ahead and did it.  It's in the source code repository now so it will be in future packages.

But you should also be able to test out the new version (attached) by replacing the file of the same name in lib/Slicer3/Plugins.

To try it, enable the first step (strips->triangles), the decimation, and the last box (triangles->strips) and it should work.

Best,
Steve

On Thu, Sep 22, 2011 at 12:59 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi Steve:

 Strange... To test the error, I generate  a model using the
segmentation of freeesurfer Bert example of the left hippocampus
(using Model Maker module)... Then I tried to decimate the hippocampus
model (such as I told you previously), and I got an empty model as
output... I send you attached the Slicer log file...

 Sincerely,


Gozalo Rojas Costa


On Thu, Sep 22, 2011 at 1:38 PM, Steve Pieper <[hidden email]> wrote:
> Hmm, that's odd - I don't have that behavior here.
>
> Looking at the source code it seems that message could happen if you have no
> triangles on the input model.  What model are you trying to decimate?
>
> -Stve
>
> On Thu, Sep 22, 2011 at 11:56 AM, Gonzalo Rojas Costa
> <[hidden email]> wrote:
>>
>> Hi Steven:
>>
>> Ok... I tested the points that you told me and it rans ok...
>>
>> But, if I try to do a Surface decimation only:
>>
>> - go to Surface Toolbox
>> -- enable Surface decimation
>> -- select tissue model as input
>> -- create new model as output
>>
>> I didn't got any model as output...  In error log I got the message:
>> "no data to decimate"...
>>
>>  Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>> On Thu, Sep 22, 2011 at 12:08 PM, Steve Pieper <[hidden email]> wrote:
>> > Hmm, interesting - I just checked and that works for me as well (ubuntu
>> > 10.04).
>> >
>> > Here's what I did to test:
>> >
>> > - download sample data (MR Head)
>> > - go to Editor and use rectangle tool to draw some label spots in label
>> > 1
>> > (tissue)
>> > - use MakeModel effect to get a model
>> > - go to Surface Toolbox
>> > -- enable normals
>> > -- select flip normals
>> > -- select tissue model as input
>> > -- create new model as output
>> > -- apply
>> > - go to Data module and toggle visibility
>> > -- new model is 'inside out' compared to tissue model.
>> >
>> > Does that work for you?
>> >
>> > Another debug test: can you open the Python console (control-P) ?
>> >
>> > Best,
>> > Steve
>> >
>> > On Thu, Sep 22, 2011 at 10:27 AM, Gonzalo Rojas Costa
>> > <[hidden email]> wrote:
>> >>
>> >> Hi Steve:
>> >>
>> >>  I tried it in version 3.6.3 on Ubuntu 64 bits...
>> >>
>> >>  Sincerely,
>> >>
>> >>
>> >> Gonzalo Rojas Costa
>> >>
>> >>
>> >> On Thu, Sep 22, 2011 at 10:50 AM, Steve Pieper <[hidden email]>
>> >> wrote:
>> >> > Hi Gonzalo -
>> >> >
>> >> > Which version of slicer are you using?  I just tried with the current
>> >> > release (3.6.3 on window 32bit) and all worked as expected.
>> >> >
>> >> > -Steve
>> >> >
>> >> > On Wed, Sep 21, 2011 at 10:28 PM, Gonzalo Rojas Costa
>> >> > <[hidden email]> wrote:
>> >> >>
>> >> >> Hi Steve:
>> >> >>
>> >> >>  I tested the surface decimation function of  Surface Toolbox module
>> >> >> with some different mesh and different options/values of the
>> >> >> function,
>> >> >> but I didn't got any resulting mesh... Why ?...
>> >> >>
>> >> >>  Sincerely,
>> >> >>
>> >> >>
>> >> >> Gonzalo Rojas Costa
>> >> >>
>> >> >>
>> >> >> On Wed, Sep 21, 2011 at 11:33 AM, Steve Pieper <[hidden email]>
>> >> >> wrote:
>> >> >> >
>> >> >> > Hi Gonzalo -
>> >> >> >
>> >> >> >
>> >> >> > On Tue, Sep 20, 2011 at 11:45 PM, Gonzalo Rojas Costa
>> >> >> > <[hidden email]> wrote:
>> >> >> >>
>> >> >> >> Hi Steve:
>> >> >> >>
>> >> >> >>  I have the following questions about Surface Models related
>> >> >> >> modules:
>> >> >> >>
>> >> >> >> I) Label Map Smoothing module: that module smooths a specified
>> >> >> >> label
>> >> >> >> in a label map to get a better surface model ?
>> >> >> >
>> >> >> > That module was contributed by our colleagues in Utah based on a
>> >> >> > similar
>> >> >> > tool in the scirun package, so you might find some more
>> >> >> > information
>> >> >> > from
>> >> >> > their site (try google).  In general yes, the goal is to clean up
>> >> >> > ridges
>> >> >> > in
>> >> >> > the label volume to get a better model.
>> >> >> >
>> >> >> >>
>> >> >> >> II) Surface Toolbox module:
>> >> >> >> a) Surface Decimation --> Boundary vertex deletion: what it means
>> >> >> >> ?
>> >> >> >>
>> >> >> >> b) Surface Smoothing --> Which is the difference between Laplace
>> >> >> >> and
>> >> >> >> Taubin surface smoothing algorithms ?
>> >> >> >> c) Surface Normals: a more detailed explanation of each parameter
>> >> >> >> ?
>> >> >> >
>> >> >> > Ah, yes, well I guess there is more detailed info available on
>> >> >> > those
>> >> >> > topics
>> >> >> > - they refer to parameters of the underlying VTK filters which are
>> >> >> > described
>> >> >> > here:
>> >> >> >
>> >> >> >
>> >> >> > http://www.vtk.org/doc/nightly/html/classvtkDecimatePro.html#details
>> >> >> >
>> >> >> >
>> >> >> > http://www.vtk.org/doc/nightly/html/classvtkSmoothPolyDataFilter.html
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > http://www.vtk.org/doc/nightly/html/classvtkPolyDataNormals.html#details
>> >> >> >
>> >> >> > I added these links to the references section of the documentation
>> >> >> > wiki
>> >> >> > page.
>> >> >> >
>> >> >> > Thanks for the good questions!
>> >> >> > -Steve
>> >> >> >
>> >> >> >>
>> >> >> >>  Sincerely,
>> >> >> >>
>> >> >> >>
>> >> >> >> Gonzalo Rojas Costa
>> >> >> >>
>> >> >> >>
>> >> >> >> On Tue, Sep 20, 2011 at 2:08 PM, Steve Pieper
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Hi Gonzalo -
>> >> >> >> >
>> >> >> >> > That's all there is on those topics right now in terms of
>> >> >> >> > documentation.
>> >> >> >> > But if you have questions let us know.
>> >> >> >> >
>> >> >> >> > Best,
>> >> >> >> > Steve
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>


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Re: Label Map Smoothing and Surface Toolbox tutorials

Gonzalo Rojas Costa
Hi:

   I created a model, but it has some small objects separated from
others... How can I erase it?...

   Sincerely,


Gonzalo Rojas Costa


El 22-09-2011 14:43, Steve Pieper escribió:

> Ahh - interesting!  I think you found something we'd overlooked - the
> model maker turns the triangles into triangle strips for faster
> rendering, but the surface toolbox assumes things will be independent
> triangles.
>
> Turns out it was a simple thing to add the functionality so I went ahead
> and did it.  It's in the source code repository now so it will be in
> future packages.
>
> But you should also be able to test out the new version (attached) by
> replacing the file of the same name in lib/Slicer3/Plugins.
>
> To try it, enable the first step (strips->triangles), the decimation,
> and the last box (triangles->strips) and it should work.
>
> Best,
> Steve
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Re: Label Map Smoothing and Surface Toolbox tutorials

Steve Pieper
Hi Gonzalo -

Usually it's easiest to edit label maps before generating models (i.e. with the Save Island operation).

But if you are starting with models, you can try the Clip Model module to clip a model by a rectalinear box.

HTH,
Steve

On Mon, Oct 10, 2011 at 12:10 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi:

 I created a model, but it has some small objects separated from others... How can I erase it?...

 Sincerely,


Gonzalo Rojas Costa


El 22-09-2011 14:43, Steve Pieper escribió:

Ahh - interesting!  I think you found something we'd overlooked - the
model maker turns the triangles into triangle strips for faster
rendering, but the surface toolbox assumes things will be independent
triangles.

Turns out it was a simple thing to add the functionality so I went ahead
and did it.  It's in the source code repository now so it will be in
future packages.

But you should also be able to test out the new version (attached) by
replacing the file of the same name in lib/Slicer3/Plugins.

To try it, enable the first step (strips->triangles), the decimation,
and the last box (triangles->strips) and it should work.

Best,
Steve


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smoothing algorithm in grayscale model maker...

Gonzalo Rojas Costa
Hi Steve:

   Which is the smoothing algorithm implemented in the grayscale model
maker module ?... Laplacian ?...  Taubin ?...

   Sincerely,


Gonzalo Rojas Costa
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Re: smoothing algorithm in grayscale model maker...

Steve Pieper
Hi Gonzalo -

It uses a windowed sinc - I added a link the documentation:

http://www.slicer.org/slicerWiki/index.php/Modules:GrayscaleModelMaker-Documentation-3.6#References

Best,
Steve

On Sun, Oct 16, 2011 at 11:51 PM, Gonzalo Rojas Costa <[hidden email]> wrote:
Hi Steve:

 Which is the smoothing algorithm implemented in the grayscale model maker module ?... Laplacian ?...  Taubin ?...

 Sincerely,


Gonzalo Rojas Costa


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