Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

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Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Haiyong Xu-2
Hi there,

3D Slicer is now being used in our ImageLab by radiologists and
physician assistants to study coronary arteries. I get a new
requirement to see if 3D Slicer has a tool to adjust a manually drawn
boundary around a coronary artery. For example, in the "Editor"
module, after draw a boundary using the "Draw" tool icon, is there
another tool I can use to fine-tune it?

There is a tool in Osirix call "Repulsor" which is very easy to use,
and the radiologist wants to have in 3D Slicer. A video on Youtube (as
below) demonstrate what it is.

http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).

Please let me know if there is already such a tool implemented in 3D
Slicer, or is there is some classes useful in VTK that can let me I
implement it in 3D Slicer.

Thanks.

Haiyong Xu
from Wake Forest University
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Andrey Fedorov
"Smudge" function of Paint in Editor module should be what you are looking for:

http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation

On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:

> Hi there,
>
> 3D Slicer is now being used in our ImageLab by radiologists and
> physician assistants to study coronary arteries. I get a new
> requirement to see if 3D Slicer has a tool to adjust a manually drawn
> boundary around a coronary artery. For example, in the "Editor"
> module, after draw a boundary using the "Draw" tool icon, is there
> another tool I can use to fine-tune it?
>
> There is a tool in Osirix call "Repulsor" which is very easy to use,
> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
> below) demonstrate what it is.
>
> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>
> Please let me know if there is already such a tool implemented in 3D
> Slicer, or is there is some classes useful in VTK that can let me I
> implement it in 3D Slicer.
>
> Thanks.
>
> Haiyong Xu
> from Wake Forest University
> _______________________________________________
> 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
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Haiyong Xu-2
Thanks Andriy. Would you like to tell me more how to utilize the
Smudge function in order to have a similar effect of the "Repulsor"
tool in Osirix?

Probably I didn't explore it enough, the "Smudge" function of Paint
looks like a little bit different from our need. This tool is used to
paint pixels. Painting all pixels inside a coronary artery will take
too long time. What we needed is to draw artery boundaries for several
slices, interpolate boundaries for intermediate slices, and refine a
boundary by nudging it. The nudge tool will be something like pulling
an elastic string (the video on Youtube is exactly what we want). Any
suggestions of how to do it in 3D Slicer are welcome. Thanks.

Haiyong



On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:

> "Smudge" function of Paint in Editor module should be what you are looking for:
>
> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>
> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>> Hi there,
>>
>> 3D Slicer is now being used in our ImageLab by radiologists and
>> physician assistants to study coronary arteries. I get a new
>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>> boundary around a coronary artery. For example, in the "Editor"
>> module, after draw a boundary using the "Draw" tool icon, is there
>> another tool I can use to fine-tune it?
>>
>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>> below) demonstrate what it is.
>>
>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>
>> Please let me know if there is already such a tool implemented in 3D
>> Slicer, or is there is some classes useful in VTK that can let me I
>> implement it in 3D Slicer.
>>
>> Thanks.
>>
>> Haiyong Xu
>> from Wake Forest University
>> _______________________________________________
>> 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
>>
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Andrey Fedorov
Haiyong,

Paint+Smudge will work similar to regular Paint, but the paint color
will change automatically depending whether you start inside or
outside the painted region.

It will not look exactly as in Osirix in the video you sent, but the
function is essentially the same.

Have you tried the Paint/Smudge function in Slicer?

AF



On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:

> Thanks Andriy. Would you like to tell me more how to utilize the
> Smudge function in order to have a similar effect of the "Repulsor"
> tool in Osirix?
>
> Probably I didn't explore it enough, the "Smudge" function of Paint
> looks like a little bit different from our need. This tool is used to
> paint pixels. Painting all pixels inside a coronary artery will take
> too long time. What we needed is to draw artery boundaries for several
> slices, interpolate boundaries for intermediate slices, and refine a
> boundary by nudging it. The nudge tool will be something like pulling
> an elastic string (the video on Youtube is exactly what we want). Any
> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>
> Haiyong
>
>
>
> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>
>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>
>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>> Hi there,
>>>
>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>> physician assistants to study coronary arteries. I get a new
>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>> boundary around a coronary artery. For example, in the "Editor"
>>> module, after draw a boundary using the "Draw" tool icon, is there
>>> another tool I can use to fine-tune it?
>>>
>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>> below) demonstrate what it is.
>>>
>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>
>>> Please let me know if there is already such a tool implemented in 3D
>>> Slicer, or is there is some classes useful in VTK that can let me I
>>> implement it in 3D Slicer.
>>>
>>> Thanks.
>>>
>>> Haiyong Xu
>>> from Wake Forest University
>>> _______________________________________________
>>> 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
>>>
>>
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Haiyong Xu-2
Hi Andriy,

I tried the Paint/Smudge function to draw a boundary around a heart
(pretty large volume comparing to a vessel). However, the result is
not as good as the one generated by "Draw" tool. Please see the
attached two files for the difference: there are several discontinued
regions in the boundary. I guess we can use the Paint/Smudge tool to
fine-tune a boundary which is generated by the "Draw" tool.

Here is the work flow I can thought right now:
1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
2. Click "a" to apply the outline, i.e., fill the outline with a label value.
3. Adjust the opacity for Label Layer to make a background layer
visible to a user.
4. Use "Paint/Smudge" tool to refine the outline.

Please let me know your suggestions to improve this work flow. It
would be much better if we could nudge an outline before apply it.

Thanks.

Haiyong



On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:

> Haiyong,
>
> Paint+Smudge will work similar to regular Paint, but the paint color
> will change automatically depending whether you start inside or
> outside the painted region.
>
> It will not look exactly as in Osirix in the video you sent, but the
> function is essentially the same.
>
> Have you tried the Paint/Smudge function in Slicer?
>
> AF
>
>
>
> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>> Thanks Andriy. Would you like to tell me more how to utilize the
>> Smudge function in order to have a similar effect of the "Repulsor"
>> tool in Osirix?
>>
>> Probably I didn't explore it enough, the "Smudge" function of Paint
>> looks like a little bit different from our need. This tool is used to
>> paint pixels. Painting all pixels inside a coronary artery will take
>> too long time. What we needed is to draw artery boundaries for several
>> slices, interpolate boundaries for intermediate slices, and refine a
>> boundary by nudging it. The nudge tool will be something like pulling
>> an elastic string (the video on Youtube is exactly what we want). Any
>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>
>> Haiyong
>>
>>
>>
>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>
>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>
>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>> Hi there,
>>>>
>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>> physician assistants to study coronary arteries. I get a new
>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>> boundary around a coronary artery. For example, in the "Editor"
>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>> another tool I can use to fine-tune it?
>>>>
>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>> below) demonstrate what it is.
>>>>
>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>
>>>> Please let me know if there is already such a tool implemented in 3D
>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>> implement it in 3D Slicer.
>>>>
>>>> Thanks.
>>>>
>>>> Haiyong Xu
>>>> from Wake Forest University
>>>> _______________________________________________
>>>> 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
>>>>
>>>
>>
>

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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Thomas Ballinger
This is moderately on-topic, as it might be useful in Haiyong's case, although not quite what he's looking for; could a "smudge" functionality be added to the draw tool as well as the paint tool?  Our Slicer 2 holdovers lament the lack of this whenever forced to use Slicer 3.  (http://www.na-mic.org/Bug/view.php?id=907)  With such a feature, a process similar to the one displayed in the "repulsor" video; a rough outline drawn, then touching up the edges to enlarge or make the ROI smaller.  Not quite as slick as automatic radius selection based on distance from the ROI in question though.

The screenshots Haiyong's last email suggest a misunderstanding of the point of the paint module; it is not generally for drawing outlines, but for (using a larger radius) touching up an ROI.

Thomas Ballinger

On Wed, Jun 8, 2011 at 4:18 PM, Haiyong Xu <[hidden email]> wrote:
Hi Andriy,

I tried the Paint/Smudge function to draw a boundary around a heart
(pretty large volume comparing to a vessel). However, the result is
not as good as the one generated by "Draw" tool. Please see the
attached two files for the difference: there are several discontinued
regions in the boundary. I guess we can use the Paint/Smudge tool to
fine-tune a boundary which is generated by the "Draw" tool.

Here is the work flow I can thought right now:
1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
2. Click "a" to apply the outline, i.e., fill the outline with a label value.
3. Adjust the opacity for Label Layer to make a background layer
visible to a user.
4. Use "Paint/Smudge" tool to refine the outline.

Please let me know your suggestions to improve this work flow. It
would be much better if we could nudge an outline before apply it.

Thanks.

Haiyong



On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:
> Haiyong,
>
> Paint+Smudge will work similar to regular Paint, but the paint color
> will change automatically depending whether you start inside or
> outside the painted region.
>
> It will not look exactly as in Osirix in the video you sent, but the
> function is essentially the same.
>
> Have you tried the Paint/Smudge function in Slicer?
>
> AF
>
>
>
> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>> Thanks Andriy. Would you like to tell me more how to utilize the
>> Smudge function in order to have a similar effect of the "Repulsor"
>> tool in Osirix?
>>
>> Probably I didn't explore it enough, the "Smudge" function of Paint
>> looks like a little bit different from our need. This tool is used to
>> paint pixels. Painting all pixels inside a coronary artery will take
>> too long time. What we needed is to draw artery boundaries for several
>> slices, interpolate boundaries for intermediate slices, and refine a
>> boundary by nudging it. The nudge tool will be something like pulling
>> an elastic string (the video on Youtube is exactly what we want). Any
>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>
>> Haiyong
>>
>>
>>
>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>
>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>
>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>> Hi there,
>>>>
>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>> physician assistants to study coronary arteries. I get a new
>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>> boundary around a coronary artery. For example, in the "Editor"
>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>> another tool I can use to fine-tune it?
>>>>
>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>> below) demonstrate what it is.
>>>>
>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>
>>>> Please let me know if there is already such a tool implemented in 3D
>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>> implement it in 3D Slicer.
>>>>
>>>> Thanks.
>>>>
>>>> Haiyong Xu
>>>> from Wake Forest University
>>>> _______________________________________________
>>>> 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
>>>>
>>>
>>
>

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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Andrey Fedorov
In reply to this post by Haiyong Xu-2
Haiyong,

I do have a suggestion to improve your workflow.

In step 3, instead of changing the transparency of the label layer, I
suggest you switch to showing label outline. This should make user
experience more similar to what is available in OsiriX.

To switch to label outline mode, see figure D here for instructions:
http://wiki.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Other_Slice_GUI_options

Does this look better?

AF


On Wed, Jun 8, 2011 at 4:18 PM, Haiyong Xu <[hidden email]> wrote:

> Hi Andriy,
>
> I tried the Paint/Smudge function to draw a boundary around a heart
> (pretty large volume comparing to a vessel). However, the result is
> not as good as the one generated by "Draw" tool. Please see the
> attached two files for the difference: there are several discontinued
> regions in the boundary. I guess we can use the Paint/Smudge tool to
> fine-tune a boundary which is generated by the "Draw" tool.
>
> Here is the work flow I can thought right now:
> 1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
> 2. Click "a" to apply the outline, i.e., fill the outline with a label value.
> 3. Adjust the opacity for Label Layer to make a background layer
> visible to a user.
> 4. Use "Paint/Smudge" tool to refine the outline.
>
> Please let me know your suggestions to improve this work flow. It
> would be much better if we could nudge an outline before apply it.
>
> Thanks.
>
> Haiyong
>
>
>
> On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:
>> Haiyong,
>>
>> Paint+Smudge will work similar to regular Paint, but the paint color
>> will change automatically depending whether you start inside or
>> outside the painted region.
>>
>> It will not look exactly as in Osirix in the video you sent, but the
>> function is essentially the same.
>>
>> Have you tried the Paint/Smudge function in Slicer?
>>
>> AF
>>
>>
>>
>> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>>> Thanks Andriy. Would you like to tell me more how to utilize the
>>> Smudge function in order to have a similar effect of the "Repulsor"
>>> tool in Osirix?
>>>
>>> Probably I didn't explore it enough, the "Smudge" function of Paint
>>> looks like a little bit different from our need. This tool is used to
>>> paint pixels. Painting all pixels inside a coronary artery will take
>>> too long time. What we needed is to draw artery boundaries for several
>>> slices, interpolate boundaries for intermediate slices, and refine a
>>> boundary by nudging it. The nudge tool will be something like pulling
>>> an elastic string (the video on Youtube is exactly what we want). Any
>>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>>
>>> Haiyong
>>>
>>>
>>>
>>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>>
>>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>>
>>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>>> Hi there,
>>>>>
>>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>>> physician assistants to study coronary arteries. I get a new
>>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>>> boundary around a coronary artery. For example, in the "Editor"
>>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>>> another tool I can use to fine-tune it?
>>>>>
>>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>>> below) demonstrate what it is.
>>>>>
>>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>>
>>>>> Please let me know if there is already such a tool implemented in 3D
>>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>>> implement it in 3D Slicer.
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Haiyong Xu
>>>>> from Wake Forest University
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>
>>>
>>
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

madanrao
Hello all,

If you want to study Coronaries using Slicer3, the best tool is VMTK module.

http://www.slicer.org/publications/item/view/1728

I hope it helps.

AM Mohan Rao

On Thu, Jun 9, 2011 at 6:53 AM, Andriy Fedorov <[hidden email]> wrote:
Haiyong,

I do have a suggestion to improve your workflow.

In step 3, instead of changing the transparency of the label layer, I
suggest you switch to showing label outline. This should make user
experience more similar to what is available in OsiriX.

To switch to label outline mode, see figure D here for instructions:
http://wiki.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Other_Slice_GUI_options

Does this look better?

AF


On Wed, Jun 8, 2011 at 4:18 PM, Haiyong Xu <[hidden email]> wrote:
> Hi Andriy,
>
> I tried the Paint/Smudge function to draw a boundary around a heart
> (pretty large volume comparing to a vessel). However, the result is
> not as good as the one generated by "Draw" tool. Please see the
> attached two files for the difference: there are several discontinued
> regions in the boundary. I guess we can use the Paint/Smudge tool to
> fine-tune a boundary which is generated by the "Draw" tool.
>
> Here is the work flow I can thought right now:
> 1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
> 2. Click "a" to apply the outline, i.e., fill the outline with a label value.
> 3. Adjust the opacity for Label Layer to make a background layer
> visible to a user.
> 4. Use "Paint/Smudge" tool to refine the outline.
>
> Please let me know your suggestions to improve this work flow. It
> would be much better if we could nudge an outline before apply it.
>
> Thanks.
>
> Haiyong
>
>
>
> On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:
>> Haiyong,
>>
>> Paint+Smudge will work similar to regular Paint, but the paint color
>> will change automatically depending whether you start inside or
>> outside the painted region.
>>
>> It will not look exactly as in Osirix in the video you sent, but the
>> function is essentially the same.
>>
>> Have you tried the Paint/Smudge function in Slicer?
>>
>> AF
>>
>>
>>
>> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>>> Thanks Andriy. Would you like to tell me more how to utilize the
>>> Smudge function in order to have a similar effect of the "Repulsor"
>>> tool in Osirix?
>>>
>>> Probably I didn't explore it enough, the "Smudge" function of Paint
>>> looks like a little bit different from our need. This tool is used to
>>> paint pixels. Painting all pixels inside a coronary artery will take
>>> too long time. What we needed is to draw artery boundaries for several
>>> slices, interpolate boundaries for intermediate slices, and refine a
>>> boundary by nudging it. The nudge tool will be something like pulling
>>> an elastic string (the video on Youtube is exactly what we want). Any
>>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>>
>>> Haiyong
>>>
>>>
>>>
>>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>>
>>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>>
>>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>>> Hi there,
>>>>>
>>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>>> physician assistants to study coronary arteries. I get a new
>>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>>> boundary around a coronary artery. For example, in the "Editor"
>>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>>> another tool I can use to fine-tune it?
>>>>>
>>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>>> below) demonstrate what it is.
>>>>>
>>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>>
>>>>> Please let me know if there is already such a tool implemented in 3D
>>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>>> implement it in 3D Slicer.
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Haiyong Xu
>>>>> from Wake Forest University
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>
>>>
>>
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Haiyong Xu-2
In reply to this post by Andrey Fedorov
Thanks many. Switch to label outline make it much better.

If we make the radius of Smudge tool smarter based on distance from
the ROI, it is almost the same as the "repulsor" tool in Osirix.
Anyway, I believe radiologists will be happy with this workflow.

Haiyong


On Wed, Jun 8, 2011 at 9:23 PM, Andriy Fedorov <[hidden email]> wrote:

> Haiyong,
>
> I do have a suggestion to improve your workflow.
>
> In step 3, instead of changing the transparency of the label layer, I
> suggest you switch to showing label outline. This should make user
> experience more similar to what is available in OsiriX.
>
> To switch to label outline mode, see figure D here for instructions:
> http://wiki.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Other_Slice_GUI_options
>
> Does this look better?
>
> AF
>
>
> On Wed, Jun 8, 2011 at 4:18 PM, Haiyong Xu <[hidden email]> wrote:
>> Hi Andriy,
>>
>> I tried the Paint/Smudge function to draw a boundary around a heart
>> (pretty large volume comparing to a vessel). However, the result is
>> not as good as the one generated by "Draw" tool. Please see the
>> attached two files for the difference: there are several discontinued
>> regions in the boundary. I guess we can use the Paint/Smudge tool to
>> fine-tune a boundary which is generated by the "Draw" tool.
>>
>> Here is the work flow I can thought right now:
>> 1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
>> 2. Click "a" to apply the outline, i.e., fill the outline with a label value.
>> 3. Adjust the opacity for Label Layer to make a background layer
>> visible to a user.
>> 4. Use "Paint/Smudge" tool to refine the outline.
>>
>> Please let me know your suggestions to improve this work flow. It
>> would be much better if we could nudge an outline before apply it.
>>
>> Thanks.
>>
>> Haiyong
>>
>>
>>
>> On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:
>>> Haiyong,
>>>
>>> Paint+Smudge will work similar to regular Paint, but the paint color
>>> will change automatically depending whether you start inside or
>>> outside the painted region.
>>>
>>> It will not look exactly as in Osirix in the video you sent, but the
>>> function is essentially the same.
>>>
>>> Have you tried the Paint/Smudge function in Slicer?
>>>
>>> AF
>>>
>>>
>>>
>>> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>>>> Thanks Andriy. Would you like to tell me more how to utilize the
>>>> Smudge function in order to have a similar effect of the "Repulsor"
>>>> tool in Osirix?
>>>>
>>>> Probably I didn't explore it enough, the "Smudge" function of Paint
>>>> looks like a little bit different from our need. This tool is used to
>>>> paint pixels. Painting all pixels inside a coronary artery will take
>>>> too long time. What we needed is to draw artery boundaries for several
>>>> slices, interpolate boundaries for intermediate slices, and refine a
>>>> boundary by nudging it. The nudge tool will be something like pulling
>>>> an elastic string (the video on Youtube is exactly what we want). Any
>>>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>>>
>>>> Haiyong
>>>>
>>>>
>>>>
>>>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>>>
>>>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>>>
>>>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>>>> Hi there,
>>>>>>
>>>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>>>> physician assistants to study coronary arteries. I get a new
>>>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>>>> boundary around a coronary artery. For example, in the "Editor"
>>>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>>>> another tool I can use to fine-tune it?
>>>>>>
>>>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>>>> below) demonstrate what it is.
>>>>>>
>>>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>>>
>>>>>> Please let me know if there is already such a tool implemented in 3D
>>>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>>>> implement it in 3D Slicer.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Haiyong Xu
>>>>>> from Wake Forest University
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>
>>>>
>>>
>>
>
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Re: Is there a nudge tool in 3D Slicer to adjust a contour (manually drawn boundary)?

Steve Pieper
Hi Haiyong & all -

There's a new Editor effect in the slicer3 trunk (that you can try in the nightly builds) called the ModelDrawEffect.  Although it doesn't have the 'repulsor" behavior, it does have some handy interpolation features that make it handy for defining large structures by putting control points on just a few slices.  Note that it can be used with the ThresholdPaint feature, so it should be good for defining vessels in contrast enhanced scans.

It's still a bit of a work in progress, but I think it's already useful for a lot of cases.

-Steve

On Thu, Jun 9, 2011 at 9:27 AM, Haiyong Xu <[hidden email]> wrote:
Thanks many. Switch to label outline make it much better.

If we make the radius of Smudge tool smarter based on distance from
the ROI, it is almost the same as the "repulsor" tool in Osirix.
Anyway, I believe radiologists will be happy with this workflow.

Haiyong


On Wed, Jun 8, 2011 at 9:23 PM, Andriy Fedorov <[hidden email]> wrote:
> Haiyong,
>
> I do have a suggestion to improve your workflow.
>
> In step 3, instead of changing the transparency of the label layer, I
> suggest you switch to showing label outline. This should make user
> experience more similar to what is available in OsiriX.
>
> To switch to label outline mode, see figure D here for instructions:
> http://wiki.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Other_Slice_GUI_options
>
> Does this look better?
>
> AF
>
>
> On Wed, Jun 8, 2011 at 4:18 PM, Haiyong Xu <[hidden email]> wrote:
>> Hi Andriy,
>>
>> I tried the Paint/Smudge function to draw a boundary around a heart
>> (pretty large volume comparing to a vessel). However, the result is
>> not as good as the one generated by "Draw" tool. Please see the
>> attached two files for the difference: there are several discontinued
>> regions in the boundary. I guess we can use the Paint/Smudge tool to
>> fine-tune a boundary which is generated by the "Draw" tool.
>>
>> Here is the work flow I can thought right now:
>> 1. In the Editor module, use "Draw" tool to draw an outline around a ROI.
>> 2. Click "a" to apply the outline, i.e., fill the outline with a label value.
>> 3. Adjust the opacity for Label Layer to make a background layer
>> visible to a user.
>> 4. Use "Paint/Smudge" tool to refine the outline.
>>
>> Please let me know your suggestions to improve this work flow. It
>> would be much better if we could nudge an outline before apply it.
>>
>> Thanks.
>>
>> Haiyong
>>
>>
>>
>> On Wed, Jun 8, 2011 at 2:41 PM, Andriy Fedorov <[hidden email]> wrote:
>>> Haiyong,
>>>
>>> Paint+Smudge will work similar to regular Paint, but the paint color
>>> will change automatically depending whether you start inside or
>>> outside the painted region.
>>>
>>> It will not look exactly as in Osirix in the video you sent, but the
>>> function is essentially the same.
>>>
>>> Have you tried the Paint/Smudge function in Slicer?
>>>
>>> AF
>>>
>>>
>>>
>>> On Wed, Jun 8, 2011 at 2:26 PM, Haiyong Xu <[hidden email]> wrote:
>>>> Thanks Andriy. Would you like to tell me more how to utilize the
>>>> Smudge function in order to have a similar effect of the "Repulsor"
>>>> tool in Osirix?
>>>>
>>>> Probably I didn't explore it enough, the "Smudge" function of Paint
>>>> looks like a little bit different from our need. This tool is used to
>>>> paint pixels. Painting all pixels inside a coronary artery will take
>>>> too long time. What we needed is to draw artery boundaries for several
>>>> slices, interpolate boundaries for intermediate slices, and refine a
>>>> boundary by nudging it. The nudge tool will be something like pulling
>>>> an elastic string (the video on Youtube is exactly what we want). Any
>>>> suggestions of how to do it in 3D Slicer are welcome. Thanks.
>>>>
>>>> Haiyong
>>>>
>>>>
>>>>
>>>> On Wed, Jun 8, 2011 at 1:00 PM, Andriy Fedorov <[hidden email]> wrote:
>>>>> "Smudge" function of Paint in Editor module should be what you are looking for:
>>>>>
>>>>> http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation
>>>>>
>>>>> On Wed, Jun 8, 2011 at 12:11 PM, Haiyong Xu <[hidden email]> wrote:
>>>>>> Hi there,
>>>>>>
>>>>>> 3D Slicer is now being used in our ImageLab by radiologists and
>>>>>> physician assistants to study coronary arteries. I get a new
>>>>>> requirement to see if 3D Slicer has a tool to adjust a manually drawn
>>>>>> boundary around a coronary artery. For example, in the "Editor"
>>>>>> module, after draw a boundary using the "Draw" tool icon, is there
>>>>>> another tool I can use to fine-tune it?
>>>>>>
>>>>>> There is a tool in Osirix call "Repulsor" which is very easy to use,
>>>>>> and the radiologist wants to have in 3D Slicer. A video on Youtube (as
>>>>>> below) demonstrate what it is.
>>>>>>
>>>>>> http://www.youtube.com/watch?v=9-FHUvl9NE4  (between 3:00 and 3:30).
>>>>>>
>>>>>> Please let me know if there is already such a tool implemented in 3D
>>>>>> Slicer, or is there is some classes useful in VTK that can let me I
>>>>>> implement it in 3D Slicer.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Haiyong Xu
>>>>>> from Wake Forest University
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>
>>>>
>>>
>>
>
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