Draw 2 slices, fill the others in Slicer

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Draw 2 slices, fill the others in Slicer

Dorian P.
Hello everyone,

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

Thank you.


P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.


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Re: Draw 2 slices, fill the others in Slicer

Andras Lasso-2

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 


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Re: Draw 2 slices, fill the others in Slicer

Dorian P.
In reply to this post by Dorian P.
Thank you Andras,

It looks really easy, the only problem is my lesions can be complex shapes. When I click inside the model it does not update it with an internal concave deviation, it has the tendency to create larger convex points. Is this normal or am I missing something?

Is there any of the many modules that can take a partial segmentation niftii with missing slices, and create an isoline/model of it to fill only the missing slices? This would be helpful also because I have already the partial segmentatons drawn in ITKsnap.

Thank you.

On Thu, Jun 18, 2015 at 2:51 PM, Andras Lasso <[hidden email]> wrote:

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 



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Re: Draw 2 slices, fill the others in Slicer

Steve Pieper-2
Hi Dorian - 

I did a tool in slicer3 that might be useful for what you are doing.  You can see videos here:


We've been meaning to port it to slicer4 for quite a while but it just hasn't happened yet:

http://www.na-mic.org/Bug/bug_view_advanced_page.php?bug_id=2322

If you want to try to use slicer3 it should still work.

Best,
Steve

On Fri, Jun 19, 2015 at 9:48 AM, Dorian P. <[hidden email]> wrote:
Thank you Andras,

It looks really easy, the only problem is my lesions can be complex shapes. When I click inside the model it does not update it with an internal concave deviation, it has the tendency to create larger convex points. Is this normal or am I missing something?

Is there any of the many modules that can take a partial segmentation niftii with missing slices, and create an isoline/model of it to fill only the missing slices? This would be helpful also because I have already the partial segmentatons drawn in ITKsnap.

Thank you.

On Thu, Jun 18, 2015 at 2:51 PM, Andras Lasso <[hidden email]> wrote:

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 



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Re: Draw 2 slices, fill the others in Slicer

Andrey Fedorov-2
In reply to this post by Dorian P.

You tried Dilate or Dilate+erode for closing effects from editor, right?

If you want to fill few missing slices, it may be perfect.

---
Sent from my mobile device

On Jun 19, 2015 9:49 AM, "Dorian P." <[hidden email]> wrote:
Thank you Andras,

It looks really easy, the only problem is my lesions can be complex shapes. When I click inside the model it does not update it with an internal concave deviation, it has the tendency to create larger convex points. Is this normal or am I missing something?

Is there any of the many modules that can take a partial segmentation niftii with missing slices, and create an isoline/model of it to fill only the missing slices? This would be helpful also because I have already the partial segmentatons drawn in ITKsnap.

Thank you.

On Thu, Jun 18, 2015 at 2:51 PM, Andras Lasso <[hidden email]> wrote:

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: Draw 2 slices, fill the others in Slicer

Andras Lasso-2
In reply to this post by Dorian P.

The ability follow concavities is limited. So, you can only use this method for shapes that do not have strong concavities.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Friday, June 19, 2015 9:49 AM
To: Andras Lasso
Cc: SPL Slicer Users
Subject: Re: Draw 2 slices, fill the others in Slicer

 

Thank you Andras,

 

It looks really easy, the only problem is my lesions can be complex shapes. When I click inside the model it does not update it with an internal concave deviation, it has the tendency to create larger convex points. Is this normal or am I missing something?

 

Is there any of the many modules that can take a partial segmentation niftii with missing slices, and create an isoline/model of it to fill only the missing slices? This would be helpful also because I have already the partial segmentatons drawn in ITKsnap.

 

Thank you.

 

On Thu, Jun 18, 2015 at 2:51 PM, Andras Lasso <[hidden email]> wrote:

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 

 


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Re: Draw 2 slices, fill the others in Slicer

Dorian P.
In reply to this post by Dorian P.
Thanks a lot to everyone who commented.

Steve, the tool looks very nice, I might install Slicer3 and give it a try. In the video you show the same six points you set at all slices. Do I need to keep the same number of points from slice to slice? My brain lesions have complex shapes, sometimes splitting and joining, and islands of normal tissue in the middle of a lesion are present in a slice. 

Andrey, I am affraid dilate-erode cycles will make the shape rounder, i.e., the narrow channels will be filled and there is not way to recover them.

Dorian


On Fri, Jun 19, 2015 at 9:54 AM, Steve Pieper <[hidden email]> wrote:
Hi Dorian - 

I did a tool in slicer3 that might be useful for what you are doing.  You can see videos here:


We've been meaning to port it to slicer4 for quite a while but it just hasn't happened yet:

http://www.na-mic.org/Bug/bug_view_advanced_page.php?bug_id=2322

If you want to try to use slicer3 it should still work.

Best,
Steve

On Fri, Jun 19, 2015 at 9:48 AM, Dorian P. <[hidden email]> wrote:
Thank you Andras,

It looks really easy, the only problem is my lesions can be complex shapes. When I click inside the model it does not update it with an internal concave deviation, it has the tendency to create larger convex points. Is this normal or am I missing something?

Is there any of the many modules that can take a partial segmentation niftii with missing slices, and create an isoline/model of it to fill only the missing slices? This would be helpful also because I have already the partial segmentatons drawn in ITKsnap.

Thank you.

On Thu, Jun 18, 2015 at 2:51 PM, Andras Lasso <[hidden email]> wrote:

Try the “Volume clip with model” module (in Volume Clip extension).

 

It allows you to create segmentation by contouring on a few slices by dropping a couple of markup points. It generates/updates a surface in real-time and writes the output to an image when you click Apply.

 

See 1-minute example video:

https://www.youtube.com/watch?v=1mYNwJbE7dQ

 

Details are described in the module documentation:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dorian P.
Sent: Thursday, June 18, 2015 2:43 PM
To: SPL Slicer Users
Subject: [slicer-users] Draw 2 slices, fill the others in Slicer

 

Hello everyone,

 

I am trying to resolve a very specific problem. I have some high resolution T1 images with lesions. Drawing lesions on each slice makes little sense as they don't change too much. I would like to draw lesions on every 3-4 slices and use some method to interpolate slices in between. I know Slicer has some tools that creates isolines, but I'm not sure whether this solution will work. Any idea if Slicer will help at all? Other suggestions outside of Slicer are welcome too, as long as the interpolation makes sense.

 

My colleagues before used to downsample the image, draw it, and upsample again. I don't think this is better than simply copying the same drawing on subsequent slices. I am hoping to get something more realistic.

 

Thank you.

 

 

P.s. Autocad has an interesting function to interpolate but is very slow and impractical, not to mention it's not made to load nifti files.

 



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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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but does not contain patient information, please contact the sender and properly
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Re: Draw 2 slices, fill the others in Slicer

Attila Nagy
(Dunno if this makes it to the list...)

Hi Dorian,

the number of points has to be the same. If not, you will lose the intepolation (until you delete the extra ones; then things go back to normal).
The best practice is to start at the slice where the shape the most complex is/or the area the biggest is and then advance towards superior/inferior.
If the structures have more unconnected volumes then maybe the best practice is to create separate labels for them (since the tool interpolates, so no disconnected regions...) and then change the (disconnected) labels with the editor tool (changelabel), or I think there is a changeisland tool too...

Normal tissue can be segmented out by setting a threshold and then "use it for paint" and then "apply" the curves, so then only the the pixels belonging into the threshold range you have set will be painted.

You also have the "apply in segmented" option that yields similar results.

This tool is nice! :)

Best,
Attila

--------------------------------------------
15. 6. 19, Pént. napon Dorian P. <[hidden email]> ezt írta:

 Tárgy: Re: [slicer-users] Draw 2 slices, fill the others in Slicer
 Címzett:: "Steve Pieper" <[hidden email]>
 Másolat: "SPL Slicer Users" <[hidden email]>
 Dátum: 2015. június. 19., Péntek, 22:26
   
 
 
 Thanks a lot to everyone who commented.
 
 
 Steve, the tool looks very nice, I might install
 Slicer3 and give it a try. In the video you show the same
 six points you set at all slices. Do I need to keep the same
 number of points from slice to slice? My brain lesions
 have complex shapes, sometimes
  splitting and joining, and islands of normal tissue in the
 middle of a lesion are present in a slice. 
 
 
 
 Andrey, I am affraid dilate-erode cycles will make the
 shape rounder, i.e., the narrow channels will be filled and
 there is not way to recover them.
 
 
 
 Dorian
 
 
 
 
 
 On Fri, Jun 19, 2015
 at 9:54 AM, Steve Pieper
 <[hidden email]>
 wrote:
 
 
 
 Hi Dorian - 
 
 
 
 I did a tool in slicer3 that might be useful for what
 you are doing.  You can see videos here:
 
 
 
 https://dl.dropbox.com/u/1686930/IMAT-2011-09-23/index.html
 
 
 
 
 
 We've been meaning to port it to slicer4 for quite
 a while but it just hasn't happened yet:
 
 
 
 http://www.na-mic.org/Bug/bug_view_advanced_page.php?bug_id=2322
 
 
 
 
 If you want to try to use slicer3 it should still
 work.
 
 
 
 Best,
 Steve
 
 
 
 
 
 On Fri, Jun 19, 2015 at 9:48 AM, Dorian P. <[hidden email]>
 wrote:
 
 
 
 
 
 
 
 Thank you Andras,
 
 
 
 It looks really easy, the only problem is my lesions
 can be complex shapes. When I click inside the model it does
 not update it with an internal concave deviation, it has the
 tendency to create larger convex points. Is this normal or
 am I missing something?
 
 
 
 Is there any of the many modules that can take a
 partial segmentation niftii with missing slices, and create
 an isoline/model of it to fill only the missing slices? This
 would be helpful also because I have already the partial
 segmentatons drawn in ITKsnap.
 
 
 
 Thank you.
 
 
 
 On Thu, Jun 18,
 2015 at 2:51 PM, Andras Lasso
 <[hidden email]>
 wrote:
 
 
 
 
 
 Try the “Volume clip
 with model” module (in Volume Clip
 extension).
  
 It allows you to create
 
 segmentation by contouring on a few slices by dropping a
 couple of markup points. It generates/updates a surface in
 real-time and writes the output to an image when you click
 Apply.
  
 See 1-minute example
 video:
 https://www.youtube.com/watch?v=1mYNwJbE7dQ
  
 Details are described in
 the module documentation:
 http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip
  
 Andras
  
 
 
 From:
 [hidden email]
 [mailto:[hidden email]]
 On Behalf Of Dorian P.
 
 Sent: Thursday, June 18, 2015 2:43 PM
 
 To: SPL Slicer Users
 
 Subject: [slicer-users] Draw 2 slices, fill the
 others in Slicer
 
 
 
 
 
  
 
 Hello everyone,
 
 
 
 
  
 
 
 I am trying to resolve a
 very specific problem. I have some high resolution T1 images
 with lesions. Drawing lesions on each slice makes little
 sense as they don't change too much. I would like to
 draw lesions on every 3-4 slices and use
  some method to interpolate slices in between. I know Slicer
 has some tools that creates isolines, but I'm not sure
 whether this solution will work. Any idea if Slicer will
 help at all? Other suggestions outside of Slicer are welcome
 too, as long as the interpolation
  makes sense.
 
 
  
 
 
 My colleagues before used
 to downsample the image, draw it, and upsample again. I
 don't think this is better than simply copying the same
 drawing on subsequent slices. I am hoping to get something
 more realistic.
 
 
  
 
 
 Thank
 you.
 
 
  
 
 
  
 
 
 P.s. Autocad has an
 interesting function to interpolate but is very slow and
 impractical, not to mention it's not made to load nifti
 files.
 
 
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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Re: Draw 2 slices, fill the others in Slicer

Steve Pieper-2
In reply to this post by Dorian P.
I hope Attila's note made it to the list as there's been some config issue that was dropping his emails - can anyone confirm or deny they got his email below through the mailing list?

Also, Dorian, on the issue of branching and merging, using ModelDraw you would just create multiple interpolation in the same label color for the branching structures and they get merged back when you do the model building step.  For the islands of normal tissue you can (maybe) use the threshold paint to exclude them or you can do a separate step where you define a ModelDraw shape in background color.

-Steve

On Fri, Jun 19, 2015 at 4:35 PM, Attila Nagy <[hidden email]> wrote:
(Dunno if this makes it to the list...)

Hi Dorian,

the number of points has to be the same. If not, you will lose the intepolation (until you delete the extra ones; then things go back to normal).
The best practice is to start at the slice where the shape the most complex is/or the area the biggest is and then advance towards superior/inferior.
If the structures have more unconnected volumes then maybe the best practice is to create separate labels for them (since the tool interpolates, so no disconnected regions...) and then change the (disconnected) labels with the editor tool (changelabel), or I think there is a changeisland tool too...

Normal tissue can be segmented out by setting a threshold and then "use it for paint" and then "apply" the curves, so then only the the pixels belonging into the threshold range you have set will be painted.

You also have the "apply in segmented" option that yields similar results.

This tool is nice! :)

Best,
Attila

--------------------------------------------
15. 6. 19, Pént. napon Dorian P. <[hidden email]> ezt írta:

 Tárgy: Re: [slicer-users] Draw 2 slices, fill the others in Slicer
 Címzett:: "Steve Pieper" <[hidden email]>
 Másolat: "SPL Slicer Users" <[hidden email]>
 Dátum: 2015. június. 19., Péntek, 22:26



 Thanks a lot to everyone who commented.


 Steve, the tool looks very nice, I might install
 Slicer3 and give it a try. In the video you show the same
 six points you set at all slices. Do I need to keep the same
 number of points from slice to slice? My brain lesions
 have complex shapes, sometimes
  splitting and joining, and islands of normal tissue in the
 middle of a lesion are present in a slice. 



 Andrey, I am affraid dilate-erode cycles will make the
 shape rounder, i.e., the narrow channels will be filled and
 there is not way to recover them.



 Dorian





 On Fri, Jun 19, 2015
 at 9:54 AM, Steve Pieper
 <[hidden email]>
 wrote:



 Hi Dorian - 



 I did a tool in slicer3 that might be useful for what
 you are doing.  You can see videos here:



 https://dl.dropbox.com/u/1686930/IMAT-2011-09-23/index.html





 We've been meaning to port it to slicer4 for quite
 a while but it just hasn't happened yet:



 http://www.na-mic.org/Bug/bug_view_advanced_page.php?bug_id=2322




 If you want to try to use slicer3 it should still
 work.



 Best,
 Steve





 On Fri, Jun 19, 2015 at 9:48 AM, Dorian P. <[hidden email]>
 wrote:







 Thank you Andras,



 It looks really easy, the only problem is my lesions
 can be complex shapes. When I click inside the model it does
 not update it with an internal concave deviation, it has the
 tendency to create larger convex points. Is this normal or
 am I missing something?



 Is there any of the many modules that can take a
 partial segmentation niftii with missing slices, and create
 an isoline/model of it to fill only the missing slices? This
 would be helpful also because I have already the partial
 segmentatons drawn in ITKsnap.



 Thank you.



 On Thu, Jun 18,
 2015 at 2:51 PM, Andras Lasso
 <[hidden email]>
 wrote:





 Try the “Volume clip
 with model” module (in Volume Clip
 extension).
  
 It allows you to create

 segmentation by contouring on a few slices by dropping a
 couple of markup points. It generates/updates a surface in
 real-time and writes the output to an image when you click
 Apply.
  
 See 1-minute example
 video:
 https://www.youtube.com/watch?v=1mYNwJbE7dQ
  
 Details are described in
 the module documentation:
 http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/VolumeClip
  
 Andras
  


 From:
 [hidden email]
 [mailto:[hidden email]]
 On Behalf Of Dorian P.

 Sent: Thursday, June 18, 2015 2:43 PM

 To: SPL Slicer Users

 Subject: [slicer-users] Draw 2 slices, fill the
 others in Slicer





  

 Hello everyone,




  


 I am trying to resolve a
 very specific problem. I have some high resolution T1 images
 with lesions. Drawing lesions on each slice makes little
 sense as they don't change too much. I would like to
 draw lesions on every 3-4 slices and use
  some method to interpolate slices in between. I know Slicer
 has some tools that creates isolines, but I'm not sure
 whether this solution will work. Any idea if Slicer will
 help at all? Other suggestions outside of Slicer are welcome
 too, as long as the interpolation
  makes sense.


  


 My colleagues before used
 to downsample the image, draw it, and upsample again. I
 don't think this is better than simply copying the same
 drawing on subsequent slices. I am hoping to get something
 more realistic.


  


 Thank
 you.


  


  


 P.s. Autocad has an
 interesting function to interpolate but is very slow and
 impractical, not to mention it's not made to load nifti
 files.


  


















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