question ? [convertion mesh to binary image]

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question ? [convertion mesh to binary image]

agatte
Hi,

Is there any possibility to make convertion model( triangle mesh) to binary image (mhd, mha)  in slicer ?

I would appreciate for any help/ advice.


Best,
Agata

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Re: question ? [convertion mesh to binary image]

Csaba Pinter-2

Hi Agata,

 

There is the model to label map module in Slicer core, which can do that, but it has rather big limitations.

 

What I suggest is to use SlicerRT’s contour mechanism. You load your model, create a contour from the model (see HowTo section on page [1]), and convert it to labelmap in the Contours module. Then you can save the labelmap to any desired format.

 

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Contours

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Agata Krason
Sent: Sunday, March 23, 2014 04:59
To: [hidden email]
Subject: [slicer-users] question ? [convertion mesh to binary image]

 

Hi,

 

Is there any possibility to make convertion model( triangle mesh) to binary image (mhd, mha)  in slicer ?

 

I would appreciate for any help/ advice.

 

 

Best,

Agata


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Re: question ? [convertion mesh to binary image]

agatte
Hi Csaba,


Thanks for Your reply.  But it doesn't work in my case.
I have only a model as vtk (polydata triangle mesh). 
It is required  to have model + ref volume to create labelmap in "Contours" RTSlicer. 

Agata


2014-03-23 13:42 GMT+01:00 Csaba Pinter <[hidden email]>:

Hi Agata,

 

There is the model to label map module in Slicer core, which can do that, but it has rather big limitations.

 

What I suggest is to use SlicerRT’s contour mechanism. You load your model, create a contour from the model (see HowTo section on page [1]), and convert it to labelmap in the Contours module. Then you can save the labelmap to any desired format.

 

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Contours

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Agata Krason
Sent: Sunday, March 23, 2014 04:59
To: [hidden email]
Subject: [slicer-users] question ? [convertion mesh to binary image]

 

Hi,

 

Is there any possibility to make convertion model( triangle mesh) to binary image (mhd, mha)  in slicer ?

 

I would appreciate for any help/ advice.

 

 

Best,

Agata



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Re: question ? [convertion mesh to binary image]

Csaba Pinter-2

You cannot expect to be able to convert it to a labelmap if you don’t specify its lattice. You’ll need a volume that overlaps with your model in order to convert it to labelmap.

 

csaba

 

From: Agata Krasoń [mailto:[hidden email]]
Sent: Sunday, March 23, 2014 10:52
To: Csaba Pinter; [hidden email]
Subject: Re: [slicer-users] question ? [convertion mesh to binary image]

 

Hi Csaba,

 

 

Thanks for Your reply.  But it doesn't work in my case.

I have only a model as vtk (polydata triangle mesh). 

It is required  to have model + ref volume to create labelmap in "Contours" RTSlicer. 

 

Agata

 

2014-03-23 13:42 GMT+01:00 Csaba Pinter <[hidden email]>:

Hi Agata,

 

There is the model to label map module in Slicer core, which can do that, but it has rather big limitations.

 

What I suggest is to use SlicerRT’s contour mechanism. You load your model, create a contour from the model (see HowTo section on page [1]), and convert it to labelmap in the Contours module. Then you can save the labelmap to any desired format.

 

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Contours

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Agata Krason
Sent: Sunday, March 23, 2014 04:59
To: [hidden email]
Subject: [slicer-users] question ? [convertion mesh to binary image]

 

Hi,

 

Is there any possibility to make convertion model( triangle mesh) to binary image (mhd, mha)  in slicer ?

 

I would appreciate for any help/ advice.

 

 

Best,

Agata

 


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Re: question ? [convertion mesh to binary image]

Andrey Fedorov
You can use CropVolume module to create a reference volume. Just load
any image, and use CropVolume to define the ROI enclosing your surface
model, and then apply crop. The ROI can be completely outside the FOV
of the volume you are cropping, outside voxels will be filled with the
default value. This is not the "intended" use of CropVolume, but I
think it can serve your need.

On Sun, Mar 23, 2014 at 12:12 PM, Csaba Pinter <[hidden email]> wrote:

> You cannot expect to be able to convert it to a labelmap if you don’t
> specify its lattice. You’ll need a volume that overlaps with your model in
> order to convert it to labelmap.
>
>
>
> csaba
>
>
>
> From: Agata Krasoń [mailto:[hidden email]]
> Sent: Sunday, March 23, 2014 10:52
> To: Csaba Pinter; [hidden email]
> Subject: Re: [slicer-users] question ? [convertion mesh to binary image]
>
>
>
> Hi Csaba,
>
>
>
>
>
> Thanks for Your reply.  But it doesn't work in my case.
>
> I have only a model as vtk (polydata triangle mesh).
>
> It is required  to have model + ref volume to create labelmap in "Contours"
> RTSlicer.
>
>
>
> Agata
>
>
>
> 2014-03-23 13:42 GMT+01:00 Csaba Pinter <[hidden email]>:
>
> Hi Agata,
>
>
>
> There is the model to label map module in Slicer core, which can do that,
> but it has rather big limitations.
>
>
>
> What I suggest is to use SlicerRT’s contour mechanism. You load your model,
> create a contour from the model (see HowTo section on page [1]), and convert
> it to labelmap in the Contours module. Then you can save the labelmap to any
> desired format.
>
>
>
> csaba
>
>
>
> [1]
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Contours
>
>
>
>
>
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Agata Krason
> Sent: Sunday, March 23, 2014 04:59
> To: [hidden email]
> Subject: [slicer-users] question ? [convertion mesh to binary image]
>
>
>
> Hi,
>
>
>
> Is there any possibility to make convertion model( triangle mesh) to binary
> image (mhd, mha)  in slicer ?
>
>
>
> I would appreciate for any help/ advice.
>
>
>
>
>
> Best,
>
> Agata
>
>
>
>
> _______________________________________________
> 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
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Image stack loading performance issue

Murat Maga
Hello,

Any ideas why it is taking Slicer a lot longer to load the same image stack, for example compared to ImageJ. And when I say longer, I mean it is about 20 times longer.

If I make the image stack into a single volume, the difference between IJ and Slicer is no longer there.

M

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Re: Image stack loading performance issue

Julien Finet
Hi Murat,

There are multiple reasons why the code is slow. The good news is that I fixed all the unnecessary bottlenecks.
I have not had a chance to push the speed-up back into Slicer trunk.
This will be fixed in the next Slicer release.

Hth,
Julien.


On Mon, Mar 24, 2014 at 1:29 PM, Murat Maga <[hidden email]> wrote:
Hello,

Any ideas why it is taking Slicer a lot longer to load the same image stack, for example compared to ImageJ. And when I say longer, I mean it is about 20 times longer.

If I make the image stack into a single volume, the difference between IJ and Slicer is no longer there.

M

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but does not contain patient information, please contact the sender and properly
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AMD GPUs and SLicer

Murat Maga

Hello,

 

Has anybody experienced issues with AMD GPUs in Slicer? We are planning to get some computers with Firepros on them and last time I have an AMD card, I ended up with some openGL issues with some other 3D software (wasn’t using Slicer at the time).

 

Thanks,

Murat

 


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Re: AMD GPUs and SLicer

Julien Finet
Hi Murat,

There used to be some Volume Rendering issues (GPU Volume Raycast Mapper) with the drivers of Apple when they were building their computers with AMD GPUs.
However, that was limited to Mac OS. I am not aware of current AMD limitation with VTK.

Hth,
Julien.


On Mon, Mar 24, 2014 at 2:44 PM, Murat Maga <[hidden email]> wrote:

Hello,

 

Has anybody experienced issues with AMD GPUs in Slicer? We are planning to get some computers with Firepros on them and last time I have an AMD card, I ended up with some openGL issues with some other 3D software (wasn’t using Slicer at the time).

 

Thanks,

Murat

 


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Re: Image stack loading performance issue

Julien Finet
In reply to this post by Julien Finet
I meant on the next stable release, but I actually ended up pushing the fixes.
So this should be available in the next nightlies (-> r23019).

Hth,
Julien.


On Mon, Mar 24, 2014 at 5:35 PM, <[hidden email]> wrote:
Hi Julien,
Are you referring to next version of the stable release or the nightlies?



From: [hidden email]
Sent: Monday, March 24, 2014 10:55 AM
To: [hidden email]
Cc: [hidden email]

Hi Murat,

There are multiple reasons why the code is slow. The good news is that I fixed all the unnecessary bottlenecks.
I have not had a chance to push the speed-up back into Slicer trunk.
This will be fixed in the next Slicer release.

Hth,
Julien.


On Mon, Mar 24, 2014 at 1:29 PM, Murat Maga <[hidden email]> wrote:
Hello,

Any ideas why it is taking Slicer a lot longer to load the same image stack, for example compared to ImageJ. And when I say longer, I mean it is about 20 times longer.

If I make the image stack into a single volume, the difference between IJ and Slicer is no longer there.

M

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