Again about the nasal cavity reconstruction

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Again about the nasal cavity reconstruction

Samuele Zampini
Dear all,

I am still fighting against the nasal cavity reconstruction. The point is that I
tried to follow both your advice and the tutorials, but I can not do everything
as I would like to.

The first question is: to select only the air into the nasal cavity, I placed a plane
at the inlet of the airflows (where there are the nostrils - fig. inlet.png) and another
 one at the outlet of the trachea (not sure that is the trachea, sorry!,
fig. outlet.png)..

Later, and that's the second question, what I would like to do is to select the air
between these 2 planes (that's to say the inside of the nasal cavity!).
Which is the right feature that allows me to get the result I am looking for??
Is a button shown in the pictures attached or it belongs to another module?
The reason I can not succeed in doing this operation is that I try with a
threshold, but it let me select the whole black volume, not only the inside of
the nasal cavity, between the 2 "planes" I fixed!

Also, about the "air": I think there's a filter that helps to select the black-volume,
i.e. the air. Could you let me know its name?

Hope you can help,

thanks in advance,


--
                                                                                                         Samuele
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
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Re: Again about the nasal cavity reconstruction

Aucoin, Nicole
Hello,

I think that using the Crop Volume module will be helpful - you can
select just the part of your volume that you want to segment, aligning
the edges of the crop to line up with the planes that you defined.
Modules->Converters->Crop Volume
On the ROI drop down, create a new ROI node.
Set the output volume to Create a New Volume.
Show all the slices in 3D and adjust the ROI handles until the shaded
box in the slices matches the region you wish to crop out around the
nasal passages (you can slide the slice sliders to show different slices
while you're adjusting the ROI box in 3D).
Click on "Do ROI Resample"

Now you can use this smaller volume as input for editing and segmentation.
You can pass it as the input to the Filtering->Threshold Image module
which will let you set both upper and lower thresholds for the input
volume.  You can use the Filtering->Arithmetic->Mask Image to apply this
thresholded image as a mask to the original image (though you might have
to save the thresholded image and reload it as a label map).

There are a number of different automated segmentation algorithms under
Modules->Segmentation, one of them might work well for your case.

Nicole

Sammy wrote:

> Dear all,
>
> I am still fighting against the nasal cavity reconstruction. The point
> is that I
> tried to follow both your advice and the tutorials, but I can not do
> everything
> as I would like to.
>
> The first question is: to select only the air into the nasal cavity, I
> placed a plane
> at the inlet of the airflows (where there are the nostrils - fig.
> inlet.png) and another
>  one at the outlet of the trachea (not sure that is the trachea, sorry!,
> fig. outlet.png)..
>
> Later, and that's the second question, what I would like to do is to
> select the air
> between these 2 planes (that's to say the inside of the nasal cavity!).
> Which is the right feature that allows me to get the result I am
> looking for??
> Is a button shown in the pictures attached or it belongs to another
> module?
> The reason I can not succeed in doing this operation is that I try with a
> threshold, but it let me select the whole black volume, not only the
> inside of
> the nasal cavity, between the 2 "planes" I fixed!
>
> Also, about the "air": I think there's a filter that helps to select
> the black-volume,
> i.e. the air. Could you let me know its name?
>
> Hope you can help,
>
> thanks in advance,
>
>
> --
>                                                                      
>                                    Samuele
> ____________________________________________________________________
>
>   .~.                              
>   /V\       L   I   N   U   X    
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
> <mailto:[hidden email]>
>  home        :   +390331823927       www:   samiam1000.spaces.live.com
> <http://samiam1000.spaces.live.com>
>
>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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: Again about the nasal cavity reconstruction

Daniel Haehn
In reply to this post by Samuele Zampini
Hi Samuele,

another approach would be to use the VMTKEasyLevelSetSegmentation module.

You can specify the right threshold for the air, you want to segment. F.e. use source seeds which are the starting points of the front propagation and target seeds where the propagation will stop. Just play around a little bit.

HTH,
Daniel

On Oct 15, 2010, at 12:30 PM, Sammy wrote:

> Dear all,
>
> I am still fighting against the nasal cavity reconstruction. The point is that I
> tried to follow both your advice and the tutorials, but I can not do everything
> as I would like to.
>
> The first question is: to select only the air into the nasal cavity, I placed a plane
> at the inlet of the airflows (where there are the nostrils - fig. inlet.png) and another
>  one at the outlet of the trachea (not sure that is the trachea, sorry!,
> fig. outlet.png)..
>
> Later, and that's the second question, what I would like to do is to select the air
> between these 2 planes (that's to say the inside of the nasal cavity!).
> Which is the right feature that allows me to get the result I am looking for??
> Is a button shown in the pictures attached or it belongs to another module?
> The reason I can not succeed in doing this operation is that I try with a
> threshold, but it let me select the whole black volume, not only the inside of
> the nasal cavity, between the 2 "planes" I fixed!
>
> Also, about the "air": I think there's a filter that helps to select the black-volume,
> i.e. the air. Could you let me know its name?
>
> Hope you can help,
>
> thanks in advance,
>
>
> --
>                                                                                                          Samuele
> ____________________________________________________________________
>
>   .~.                              
>   /V\       L   I   N   U   X    
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>
> <inlet.png><outlet.png>_______________________________________________
> 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: Again about the nasal cavity reconstruction

Andrey Fedorov
In reply to this post by Aucoin, Nicole
On Fri, Oct 15, 2010 at 14:50, Nicole Aucoin <[hidden email]> wrote:

> Hello,
>
> I think that using the Crop Volume module will be helpful - you can
> select just the part of your volume that you want to segment, aligning
> the edges of the crop to line up with the planes that you defined.
> Modules->Converters->Crop Volume
> On the ROI drop down, create a new ROI node.
> Set the output volume to Create a New Volume.
> Show all the slices in 3D and adjust the ROI handles until the shaded
> box in the slices matches the region you wish to crop out around the
> nasal passages (you can slide the slice sliders to show different slices
> while you're adjusting the ROI box in 3D).
> Click on "Do ROI Resample"

Here make sure you don't change the default ("1") value for the "Input
spacing scaling constant".

If you set it to 0.5, you will effectively have to segment twice as
many slices as compared to the original volume...

http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6


>
> Now you can use this smaller volume as input for editing and segmentation.
> You can pass it as the input to the Filtering->Threshold Image module
> which will let you set both upper and lower thresholds for the input
> volume.  You can use the Filtering->Arithmetic->Mask Image to apply this
> thresholded image as a mask to the original image (though you might have
> to save the thresholded image and reload it as a label map).
>
> There are a number of different automated segmentation algorithms under
> Modules->Segmentation, one of them might work well for your case.
>
> Nicole
>
> Sammy wrote:
>> Dear all,
>>
>> I am still fighting against the nasal cavity reconstruction. The point
>> is that I
>> tried to follow both your advice and the tutorials, but I can not do
>> everything
>> as I would like to.
>>
>> The first question is: to select only the air into the nasal cavity, I
>> placed a plane
>> at the inlet of the airflows (where there are the nostrils - fig.
>> inlet.png) and another
>>  one at the outlet of the trachea (not sure that is the trachea, sorry!,
>> fig. outlet.png)..
>>
>> Later, and that's the second question, what I would like to do is to
>> select the air
>> between these 2 planes (that's to say the inside of the nasal cavity!).
>> Which is the right feature that allows me to get the result I am
>> looking for??
>> Is a button shown in the pictures attached or it belongs to another
>> module?
>> The reason I can not succeed in doing this operation is that I try with a
>> threshold, but it let me select the whole black volume, not only the
>> inside of
>> the nasal cavity, between the 2 "planes" I fixed!
>>
>> Also, about the "air": I think there's a filter that helps to select
>> the black-volume,
>> i.e. the air. Could you let me know its name?
>>
>> Hope you can help,
>>
>> thanks in advance,
>>
>>
>> --
>>
>>                                    Samuele
>> ____________________________________________________________________
>>
>>   .~.
>>   /V\       L   I   N   U   X
>>  // \\          I S    T H E
>>  /(   )\           W A Y
>>  ^^-^^
>>  cell phone :  +393473426510       e.mail:  [hidden email]
>> <mailto:[hidden email]>
>>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>> <http://samiam1000.spaces.live.com>
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
> 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: Again about the nasal cavity reconstruction

Samuele Zampini
In reply to this post by Samuele Zampini
Thank you all for your advice.
I really appreciate them all.

Just one more question to Ron (read below)..

Thanks,

Samuele

On Fri, Oct 15, 2010 at 10:59 PM, Ron Kikinis <[hidden email]> wrote:
1. threshold with value 1

You mean to threshold the whole black volume, right? I have to choose
a certain interval, right?
 
2. paint the two blocks with value 2

The two blocks are inlet and the outlet, right?
 
3. click on check points

Which are the check points? What does this mean?
 
4. select save island effect

This simply mean to click a button, I guess. Ok?
 
5. click somewhere inside the value 1 labeled volume of the para nasal sinus

Ok.. Let me try!
 


On 10/15/10 12:30 PM, Sammy wrote:
Dear all,

I am still fighting against the nasal cavity reconstruction. The point
is that I
tried to follow both your advice and the tutorials, but I can not do
everything
as I would like to.

The first question is: to select only the air into the nasal cavity, I
placed a plane
at the inlet of the airflows (where there are the nostrils - fig.
inlet.png) and another
 one at the outlet of the trachea (not sure that is the trachea, sorry!,
fig. outlet.png)..

Later, and that's the second question, what I would like to do is to
select the air
between these 2 planes (that's to say the inside of the nasal cavity!).
Which is the right feature that allows me to get the result I am looking
for??
Is a button shown in the pictures attached or it belongs to another module?
The reason I can not succeed in doing this operation is that I try with a
threshold, but it let me select the whole black volume, not only the
inside of
the nasal cavity, between the 2 "planes" I fixed!

Also, about the "air": I think there's a filter that helps to select the
black-volume,
i.e. the air. Could you let me know its name?

Hope you can help,

thanks in advance,


--

                                 Samuele
____________________________________________________________________

  .~.
  /V\       L   I   N   U   X
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail: [hidden email]
<mailto:[hidden email]>

 home        :   +390331823927       www: samiam1000.spaces.live.com
<http://samiam1000.spaces.live.com>



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



--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


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Re: Again about the nasal cavity reconstruction

Samuele Zampini
In reply to this post by Daniel Haehn


On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]> wrote:
Hi Samuele,

another approach would be to use the VMTKEasyLevelSetSegmentation module.

I will try, even tough, AFAIK, VMTK features work well when you have a vessel-like
geometry. I think that the nasal-cavity is too complex. But Ill try.

Thanks,

Samuele
 

You can specify the right threshold for the air, you want to segment. F.e. use source seeds which are the starting points of the front propagation and target seeds where the propagation will stop. Just play around a little bit.

HTH,
Daniel

On Oct 15, 2010, at 12:30 PM, Sammy wrote:

> Dear all,
>
> I am still fighting against the nasal cavity reconstruction. The point is that I
> tried to follow both your advice and the tutorials, but I can not do everything
> as I would like to.
>
> The first question is: to select only the air into the nasal cavity, I placed a plane
> at the inlet of the airflows (where there are the nostrils - fig. inlet.png) and another
>  one at the outlet of the trachea (not sure that is the trachea, sorry!,
> fig. outlet.png)..
>
> Later, and that's the second question, what I would like to do is to select the air
> between these 2 planes (that's to say the inside of the nasal cavity!).
> Which is the right feature that allows me to get the result I am looking for??
> Is a button shown in the pictures attached or it belongs to another module?
> The reason I can not succeed in doing this operation is that I try with a
> threshold, but it let me select the whole black volume, not only the inside of
> the nasal cavity, between the 2 "planes" I fixed!
>
> Also, about the "air": I think there's a filter that helps to select the black-volume,
> i.e. the air. Could you let me know its name?
>
> Hope you can help,
>
> thanks in advance,
>
>
> --
>                                                                                                          Samuele
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>
> <inlet.png><outlet.png>_______________________________________________
> 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




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


_______________________________________________
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Re: Again about the nasal cavity reconstruction

Daniel Haehn
Samuele,

for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
name it as "region growing starting from a point". There is no shape
recognition like in VMTKVesselEnhancement.

Daniel

On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
wrote:

> On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
> wrote:
>
>> Hi Samuele,
>>
>> another approach would be to use the VMTKEasyLevelSetSegmentation
> module.
>>
>
> I will try, even tough, AFAIK, VMTK features work well when you have a
> vessel-like
> geometry. I think that the nasal-cavity is too complex. But Ill try.
>
> Thanks,
>
> Samuele
>
>
>>
>> You can specify the right threshold for the air, you want to segment.
> F.e.
>> use source seeds which are the starting points of the front propagation
> and
>> target seeds where the propagation will stop. Just play around a little
> bit.
>>
>> HTH,
>> Daniel
>>
>> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>
>> > Dear all,
>> >
>> > I am still fighting against the nasal cavity reconstruction. The point
> is
>> that I
>> > tried to follow both your advice and the tutorials, but I can not do
>> everything
>> > as I would like to.
>> >
>> > The first question is: to select only the air into the nasal cavity, I
>> placed a plane
>> > at the inlet of the airflows (where there are the nostrils - fig.
>> inlet.png) and another
>> >  one at the outlet of the trachea (not sure that is the trachea,
> sorry!,
>> > fig. outlet.png)..
>> >
>> > Later, and that's the second question, what I would like to do is to
>> select the air
>> > between these 2 planes (that's to say the inside of the nasal
> cavity!).
>> > Which is the right feature that allows me to get the result I am
> looking
>> for??
>> > Is a button shown in the pictures attached or it belongs to another
>> module?
>> > The reason I can not succeed in doing this operation is that I try
> with a
>> > threshold, but it let me select the whole black volume, not only the
>> inside of
>> > the nasal cavity, between the 2 "planes" I fixed!
>> >
>> > Also, about the "air": I think there's a filter that helps to select
> the
>> black-volume,
>> > i.e. the air. Could you let me know its name?
>> >
>> > Hope you can help,
>> >
>> > thanks in advance,
>> >
>> >
>> > --
>> >
>>                                Samuele
>> > ____________________________________________________________________
>> >
>> >   .~.
>> >   /V\       L   I   N   U   X
>> >  // \\          I S    T H E
>> >  /(   )\           W A Y
>> >  ^^-^^
>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>> >  home        :   +390331823927       www:   samiam1000.spaces.live.com
>> >
>> > <inlet.png><outlet.png>_______________________________________________
>> > 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
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com

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Re: Again about the nasal cavity reconstruction

Samuele Zampini


On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn <[hidden email]> wrote:
Samuele,

for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
name it as "region growing starting from a point". There is no shape
recognition like in VMTKVesselEnhancement.

Now I'll try to follow your advice.
Thanks
 

Daniel

On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
wrote:
> On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
> wrote:
>
>> Hi Samuele,
>>
>> another approach would be to use the VMTKEasyLevelSetSegmentation
> module.
>>
>
> I will try, even tough, AFAIK, VMTK features work well when you have a
> vessel-like
> geometry. I think that the nasal-cavity is too complex. But Ill try.
>
> Thanks,
>
> Samuele
>
>
>>
>> You can specify the right threshold for the air, you want to segment.
> F.e.
>> use source seeds which are the starting points of the front propagation
> and
>> target seeds where the propagation will stop. Just play around a little
> bit.
>>
>> HTH,
>> Daniel
>>
>> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>
>> > Dear all,
>> >
>> > I am still fighting against the nasal cavity reconstruction. The point
> is
>> that I
>> > tried to follow both your advice and the tutorials, but I can not do
>> everything
>> > as I would like to.
>> >
>> > The first question is: to select only the air into the nasal cavity, I
>> placed a plane
>> > at the inlet of the airflows (where there are the nostrils - fig.
>> inlet.png) and another
>> >  one at the outlet of the trachea (not sure that is the trachea,
> sorry!,
>> > fig. outlet.png)..
>> >
>> > Later, and that's the second question, what I would like to do is to
>> select the air
>> > between these 2 planes (that's to say the inside of the nasal
> cavity!).
>> > Which is the right feature that allows me to get the result I am
> looking
>> for??
>> > Is a button shown in the pictures attached or it belongs to another
>> module?
>> > The reason I can not succeed in doing this operation is that I try
> with a
>> > threshold, but it let me select the whole black volume, not only the
>> inside of
>> > the nasal cavity, between the 2 "planes" I fixed!
>> >
>> > Also, about the "air": I think there's a filter that helps to select
> the
>> black-volume,
>> > i.e. the air. Could you let me know its name?
>> >
>> > Hope you can help,
>> >
>> > thanks in advance,
>> >
>> >
>> > --
>> >
>>                                Samuele
>> > ____________________________________________________________________
>> >
>> >   .~.
>> >   /V\       L   I   N   U   X
>> >  // \\          I S    T H E
>> >  /(   )\           W A Y
>> >  ^^-^^
>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>> >  home        :   +390331823927       www:   samiam1000.spaces.live.com
>> >
>> > <inlet.png><outlet.png>_______________________________________________
>> > 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
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


_______________________________________________
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Re: Again about the nasal cavity reconstruction

Samuele Zampini

On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn <[hidden email]> wrote:
Samuele,

for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
name it as "region growing starting from a point". There is no shape
recognition like in VMTKVesselEnhancement.

There is something strange in the results I get. Please, referring to the image attached,
I'll ask you some questions:
1. the first question is about the initialization: I think that the "colliding fronts" is the
right choice.
2. about the Source Point, I chose the red one in the picture.
3. for the Target point, actually, I would need 2 points (i.e. the 2 nostrils). Can't I
set 2 target points?
3. About the upper and lower threshold values, I think that choosing
-1000 and -500 is a good choice. The point is that as soon as I set these 2
values, everything becomes black.

Any other advice?
 

Now I'll try to follow your advice.
Thanks
 

Daniel

On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
wrote:
> On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
> wrote:
>
>> Hi Samuele,
>>
>> another approach would be to use the VMTKEasyLevelSetSegmentation
> module.
>>
>
> I will try, even tough, AFAIK, VMTK features work well when you have a
> vessel-like
> geometry. I think that the nasal-cavity is too complex. But Ill try.
>
> Thanks,
>
> Samuele
>
>
>>
>> You can specify the right threshold for the air, you want to segment.
> F.e.
>> use source seeds which are the starting points of the front propagation
> and
>> target seeds where the propagation will stop. Just play around a little
> bit.
>>
>> HTH,
>> Daniel
>>
>> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>
>> > Dear all,
>> >
>> > I am still fighting against the nasal cavity reconstruction. The point
> is
>> that I
>> > tried to follow both your advice and the tutorials, but I can not do
>> everything
>> > as I would like to.
>> >
>> > The first question is: to select only the air into the nasal cavity, I
>> placed a plane
>> > at the inlet of the airflows (where there are the nostrils - fig.
>> inlet.png) and another
>> >  one at the outlet of the trachea (not sure that is the trachea,
> sorry!,
>> > fig. outlet.png)..
>> >
>> > Later, and that's the second question, what I would like to do is to
>> select the air
>> > between these 2 planes (that's to say the inside of the nasal
> cavity!).
>> > Which is the right feature that allows me to get the result I am
> looking
>> for??
>> > Is a button shown in the pictures attached or it belongs to another
>> module?
>> > The reason I can not succeed in doing this operation is that I try
> with a
>> > threshold, but it let me select the whole black volume, not only the
>> inside of
>> > the nasal cavity, between the 2 "planes" I fixed!
>> >
>> > Also, about the "air": I think there's a filter that helps to select
> the
>> black-volume,
>> > i.e. the air. Could you let me know its name?
>> >
>> > Hope you can help,
>> >
>> > thanks in advance,
>> >
>> >
>> > --
>> >
>>                                Samuele
>> > ____________________________________________________________________
>> >
>> >   .~.
>> >   /V\       L   I   N   U   X
>> >  // \\          I S    T H E
>> >  /(   )\           W A Y
>> >  ^^-^^
>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>> >  home        :   +390331823927       www:   samiam1000.spaces.live.com
>> >
>> > <inlet.png><outlet.png>_______________________________________________
>> > 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
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


_______________________________________________
slicer-users mailing list
[hidden email]
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Re: Again about the nasal cavity reconstruction

Daniel Haehn
Please try the VMTKEasyLevelSetSegmentation instead the old, deprecated
VMTKLevelSetSegmentation.

There is also a bunch of documentation on the wiki.

HTH,
Daniel

On Sat, 16 Oct 2010 14:33:22 +0200, Sammy <[hidden email]>
wrote:

>>
>>
>> On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn
> <[hidden email]>wrote:
>>
>>> Samuele,
>>>
>>> for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
>>> name it as "region growing starting from a point". There is no shape
>>> recognition like in VMTKVesselEnhancement.
>>>
>>
> There is something strange in the results I get. Please, referring to the
> image attached,
> I'll ask you some questions:
> 1. the first question is about the initialization: I think that the
> "colliding fronts" is the
> right choice.
> 2. about the Source Point, I chose the red one in the picture.
> 3. for the Target point, actually, I would need 2 points (i.e. the 2
> nostrils). Can't I
> set 2 target points?
> 3. About the upper and lower threshold values, I think that choosing
> -1000 and -500 is a good choice. The point is that as soon as I set these
> 2
> values, everything becomes black.
>
> Any other advice?
>
>
>>
>> Now I'll try to follow your advice.
>> Thanks
>>
>>
>>>
>>> Daniel
>>>
>>> On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
>>> wrote:
>>> > On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
>>> > wrote:
>>> >
>>> >> Hi Samuele,
>>> >>
>>> >> another approach would be to use the VMTKEasyLevelSetSegmentation
>>> > module.
>>> >>
>>> >
>>> > I will try, even tough, AFAIK, VMTK features work well when you have
> a
>>> > vessel-like
>>> > geometry. I think that the nasal-cavity is too complex. But Ill try.
>>> >
>>> > Thanks,
>>> >
>>> > Samuele
>>> >
>>> >
>>> >>
>>> >> You can specify the right threshold for the air, you want to
> segment.
>>> > F.e.
>>> >> use source seeds which are the starting points of the front
> propagation
>>> > and
>>> >> target seeds where the propagation will stop. Just play around a
> little
>>> > bit.
>>> >>
>>> >> HTH,
>>> >> Daniel
>>> >>
>>> >> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>> >>
>>> >> > Dear all,
>>> >> >
>>> >> > I am still fighting against the nasal cavity reconstruction. The
>>> point
>>> > is
>>> >> that I
>>> >> > tried to follow both your advice and the tutorials, but I can not
> do
>>> >> everything
>>> >> > as I would like to.
>>> >> >
>>> >> > The first question is: to select only the air into the nasal
> cavity,
>>> I
>>> >> placed a plane
>>> >> > at the inlet of the airflows (where there are the nostrils - fig.
>>> >> inlet.png) and another
>>> >> >  one at the outlet of the trachea (not sure that is the trachea,
>>> > sorry!,
>>> >> > fig. outlet.png)..
>>> >> >
>>> >> > Later, and that's the second question, what I would like to do is
> to
>>> >> select the air
>>> >> > between these 2 planes (that's to say the inside of the nasal
>>> > cavity!).
>>> >> > Which is the right feature that allows me to get the result I am
>>> > looking
>>> >> for??
>>> >> > Is a button shown in the pictures attached or it belongs to
> another
>>> >> module?
>>> >> > The reason I can not succeed in doing this operation is that I try
>>> > with a
>>> >> > threshold, but it let me select the whole black volume, not only
> the
>>> >> inside of
>>> >> > the nasal cavity, between the 2 "planes" I fixed!
>>> >> >
>>> >> > Also, about the "air": I think there's a filter that helps to
> select
>>> > the
>>> >> black-volume,
>>> >> > i.e. the air. Could you let me know its name?
>>> >> >
>>> >> > Hope you can help,
>>> >> >
>>> >> > thanks in advance,
>>> >> >
>>> >> >
>>> >> > --
>>> >> >
>>> >>                                Samuele
>>> >> >
> ____________________________________________________________________
>>> >> >
>>> >> >   .~.
>>> >> >   /V\       L   I   N   U   X
>>> >> >  // \\          I S    T H E
>>> >> >  /(   )\           W A Y
>>> >> >  ^^-^^
>>> >> >  cell phone :  +393473426510       e.mail:
>>> [hidden email]
>>> >> >  home        :   +390331823927       www:
>>> samiam1000.spaces.live.com
>>> >> >
>>> >> >
>>> <inlet.png><outlet.png>_______________________________________________
>>> >> > 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
>>> >>
>>> >>
>>> >
>>> >
>>> > --
>>> >
>>> >              Samuele Zampini
>>> > ____________________________________________________________________
>>> >
>>> >   .~.
>>> >   /V\       L   I   N   U   X
>>> >  // \\          I S    T H E
>>> >  /(   )\           W A Y
>>> >  ^^-^^
>>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>>> >  home        :   +390331823927       www:  
> samiam1000.spaces.live.com
>>>
>>>
>>
>>
>> --
>>
>>              Samuele Zampini
>> ____________________________________________________________________
>>
>>   .~.
>>   /V\       L   I   N   U   X
>>  // \\          I S    T H E
>>  /(   )\           W A Y
>>  ^^-^^
>>  cell phone :  +393473426510       e.mail:  [hidden email]
>>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com

_______________________________________________
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Re: Again about the nasal cavity reconstruction

Samuele Zampini
Dear Daniel,

sorry if I am writing again, but I can't succeed in doing a good reconstruction.
I will now try to follow Ron's advice..

But have a look at what happens when I follow yours.

I get what you can see in the image attached.

How can I avoid to select the "outside volume"?

Thanks for your help,

Samuele



On Sat, Oct 16, 2010 at 3:46 PM, Daniel Haehn <[hidden email]> wrote:
Please try the VMTKEasyLevelSetSegmentation instead the old, deprecated
VMTKLevelSetSegmentation.

There is also a bunch of documentation on the wiki.

HTH,
Daniel

On Sat, 16 Oct 2010 14:33:22 +0200, Sammy <[hidden email]>
wrote:
>>
>>
>> On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn
> <[hidden email]>wrote:
>>
>>> Samuele,
>>>
>>> for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
>>> name it as "region growing starting from a point". There is no shape
>>> recognition like in VMTKVesselEnhancement.
>>>
>>
> There is something strange in the results I get. Please, referring to the
> image attached,
> I'll ask you some questions:
> 1. the first question is about the initialization: I think that the
> "colliding fronts" is the
> right choice.
> 2. about the Source Point, I chose the red one in the picture.
> 3. for the Target point, actually, I would need 2 points (i.e. the 2
> nostrils). Can't I
> set 2 target points?
> 3. About the upper and lower threshold values, I think that choosing
> -1000 and -500 is a good choice. The point is that as soon as I set these
> 2
> values, everything becomes black.
>
> Any other advice?
>
>
>>
>> Now I'll try to follow your advice.
>> Thanks
>>
>>
>>>
>>> Daniel
>>>
>>> On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
>>> wrote:
>>> > On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
>>> > wrote:
>>> >
>>> >> Hi Samuele,
>>> >>
>>> >> another approach would be to use the VMTKEasyLevelSetSegmentation
>>> > module.
>>> >>
>>> >
>>> > I will try, even tough, AFAIK, VMTK features work well when you have
> a
>>> > vessel-like
>>> > geometry. I think that the nasal-cavity is too complex. But Ill try.
>>> >
>>> > Thanks,
>>> >
>>> > Samuele
>>> >
>>> >
>>> >>
>>> >> You can specify the right threshold for the air, you want to
> segment.
>>> > F.e.
>>> >> use source seeds which are the starting points of the front
> propagation
>>> > and
>>> >> target seeds where the propagation will stop. Just play around a
> little
>>> > bit.
>>> >>
>>> >> HTH,
>>> >> Daniel
>>> >>
>>> >> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>> >>
>>> >> > Dear all,
>>> >> >
>>> >> > I am still fighting against the nasal cavity reconstruction. The
>>> point
>>> > is
>>> >> that I
>>> >> > tried to follow both your advice and the tutorials, but I can not
> do
>>> >> everything
>>> >> > as I would like to.
>>> >> >
>>> >> > The first question is: to select only the air into the nasal
> cavity,
>>> I
>>> >> placed a plane
>>> >> > at the inlet of the airflows (where there are the nostrils - fig.
>>> >> inlet.png) and another
>>> >> >  one at the outlet of the trachea (not sure that is the trachea,
>>> > sorry!,
>>> >> > fig. outlet.png)..
>>> >> >
>>> >> > Later, and that's the second question, what I would like to do is
> to
>>> >> select the air
>>> >> > between these 2 planes (that's to say the inside of the nasal
>>> > cavity!).
>>> >> > Which is the right feature that allows me to get the result I am
>>> > looking
>>> >> for??
>>> >> > Is a button shown in the pictures attached or it belongs to
> another
>>> >> module?
>>> >> > The reason I can not succeed in doing this operation is that I try
>>> > with a
>>> >> > threshold, but it let me select the whole black volume, not only
> the
>>> >> inside of
>>> >> > the nasal cavity, between the 2 "planes" I fixed!
>>> >> >
>>> >> > Also, about the "air": I think there's a filter that helps to
> select
>>> > the
>>> >> black-volume,
>>> >> > i.e. the air. Could you let me know its name?
>>> >> >
>>> >> > Hope you can help,
>>> >> >
>>> >> > thanks in advance,
>>> >> >
>>> >> >
>>> >> > --
>>> >> >
>>> >>                                Samuele
>>> >> >
> ____________________________________________________________________
>>> >> >
>>> >> >   .~.
>>> >> >   /V\       L   I   N   U   X
>>> >> >  // \\          I S    T H E
>>> >> >  /(   )\           W A Y
>>> >> >  ^^-^^
>>> >> >  cell phone :  +393473426510       e.mail:
>>> [hidden email]
>>> >> >  home        :   +390331823927       www:
>>> samiam1000.spaces.live.com
>>> >> >
>>> >> >
>>> <inlet.png><outlet.png>_______________________________________________
>>> >> > 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
>>> >>
>>> >>
>>> >
>>> >
>>> > --
>>> >
>>> >              Samuele Zampini
>>> > ____________________________________________________________________
>>> >
>>> >   .~.
>>> >   /V\       L   I   N   U   X
>>> >  // \\          I S    T H E
>>> >  /(   )\           W A Y
>>> >  ^^-^^
>>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>>> >  home        :   +390331823927       www:
> samiam1000.spaces.live.com
>>>
>>>
>>
>>
>> --
>>
>>              Samuele Zampini
>> ____________________________________________________________________
>>
>>   .~.
>>   /V\       L   I   N   U   X
>>  // \\          I S    T H E
>>  /(   )\           W A Y
>>  ^^-^^
>>  cell phone :  +393473426510       e.mail:  [hidden email]
>>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


_______________________________________________
slicer-users mailing list
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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Again about the nasal cavity reconstruction

Samuele Zampini
One more question about reconstructing the nasal cavity.
I finally got the model in the picture. It is neither complete
nor perfect, but I'd like to work on it.

I got this model using the VMTKEasyLevelSetSegmentation.
But how can I save a .vtk/.stl model?

Thanks a lot,

Samuele



On Sat, Oct 16, 2010 at 5:44 PM, Sammy <[hidden email]> wrote:
Dear Daniel,

sorry if I am writing again, but I can't succeed in doing a good reconstruction.
I will now try to follow Ron's advice..

But have a look at what happens when I follow yours.

I get what you can see in the image attached.

How can I avoid to select the "outside volume"?

Thanks for your help,

Samuele




On Sat, Oct 16, 2010 at 3:46 PM, Daniel Haehn <[hidden email]> wrote:
Please try the VMTKEasyLevelSetSegmentation instead the old, deprecated
VMTKLevelSetSegmentation.

There is also a bunch of documentation on the wiki.

HTH,
Daniel

On Sat, 16 Oct 2010 14:33:22 +0200, Sammy <[hidden email]>
wrote:
>>
>>
>> On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn
> <[hidden email]>wrote:
>>
>>> Samuele,
>>>
>>> for VMTKEasyLevelSetSegmentation, the geometry does not matter. You can
>>> name it as "region growing starting from a point". There is no shape
>>> recognition like in VMTKVesselEnhancement.
>>>
>>
> There is something strange in the results I get. Please, referring to the
> image attached,
> I'll ask you some questions:
> 1. the first question is about the initialization: I think that the
> "colliding fronts" is the
> right choice.
> 2. about the Source Point, I chose the red one in the picture.
> 3. for the Target point, actually, I would need 2 points (i.e. the 2
> nostrils). Can't I
> set 2 target points?
> 3. About the upper and lower threshold values, I think that choosing
> -1000 and -500 is a good choice. The point is that as soon as I set these
> 2
> values, everything becomes black.
>
> Any other advice?
>
>
>>
>> Now I'll try to follow your advice.
>> Thanks
>>
>>
>>>
>>> Daniel
>>>
>>> On Sat, 16 Oct 2010 10:44:33 +0200, Sammy <[hidden email]>
>>> wrote:
>>> > On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn <[hidden email]>
>>> > wrote:
>>> >
>>> >> Hi Samuele,
>>> >>
>>> >> another approach would be to use the VMTKEasyLevelSetSegmentation
>>> > module.
>>> >>
>>> >
>>> > I will try, even tough, AFAIK, VMTK features work well when you have
> a
>>> > vessel-like
>>> > geometry. I think that the nasal-cavity is too complex. But Ill try.
>>> >
>>> > Thanks,
>>> >
>>> > Samuele
>>> >
>>> >
>>> >>
>>> >> You can specify the right threshold for the air, you want to
> segment.
>>> > F.e.
>>> >> use source seeds which are the starting points of the front
> propagation
>>> > and
>>> >> target seeds where the propagation will stop. Just play around a
> little
>>> > bit.
>>> >>
>>> >> HTH,
>>> >> Daniel
>>> >>
>>> >> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>>> >>
>>> >> > Dear all,
>>> >> >
>>> >> > I am still fighting against the nasal cavity reconstruction. The
>>> point
>>> > is
>>> >> that I
>>> >> > tried to follow both your advice and the tutorials, but I can not
> do
>>> >> everything
>>> >> > as I would like to.
>>> >> >
>>> >> > The first question is: to select only the air into the nasal
> cavity,
>>> I
>>> >> placed a plane
>>> >> > at the inlet of the airflows (where there are the nostrils - fig.
>>> >> inlet.png) and another
>>> >> >  one at the outlet of the trachea (not sure that is the trachea,
>>> > sorry!,
>>> >> > fig. outlet.png)..
>>> >> >
>>> >> > Later, and that's the second question, what I would like to do is
> to
>>> >> select the air
>>> >> > between these 2 planes (that's to say the inside of the nasal
>>> > cavity!).
>>> >> > Which is the right feature that allows me to get the result I am
>>> > looking
>>> >> for??
>>> >> > Is a button shown in the pictures attached or it belongs to
> another
>>> >> module?
>>> >> > The reason I can not succeed in doing this operation is that I try
>>> > with a
>>> >> > threshold, but it let me select the whole black volume, not only
> the
>>> >> inside of
>>> >> > the nasal cavity, between the 2 "planes" I fixed!
>>> >> >
>>> >> > Also, about the "air": I think there's a filter that helps to
> select
>>> > the
>>> >> black-volume,
>>> >> > i.e. the air. Could you let me know its name?
>>> >> >
>>> >> > Hope you can help,
>>> >> >
>>> >> > thanks in advance,
>>> >> >
>>> >> >
>>> >> > --
>>> >> >
>>> >>                                Samuele
>>> >> >
> ____________________________________________________________________
>>> >> >
>>> >> >   .~.
>>> >> >   /V\       L   I   N   U   X
>>> >> >  // \\          I S    T H E
>>> >> >  /(   )\           W A Y
>>> >> >  ^^-^^
>>> >> >  cell phone :  +393473426510       e.mail:
>>> [hidden email]
>>> >> >  home        :   +390331823927       www:
>>> samiam1000.spaces.live.com
>>> >> >
>>> >> >
>>> <inlet.png><outlet.png>_______________________________________________
>>> >> > 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
>>> >>
>>> >>
>>> >
>>> >
>>> > --
>>> >
>>> >              Samuele Zampini
>>> > ____________________________________________________________________
>>> >
>>> >   .~.
>>> >   /V\       L   I   N   U   X
>>> >  // \\          I S    T H E
>>> >  /(   )\           W A Y
>>> >  ^^-^^
>>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>>> >  home        :   +390331823927       www:
> samiam1000.spaces.live.com
>>>
>>>
>>
>>
>> --
>>
>>              Samuele Zampini
>> ____________________________________________________________________
>>
>>   .~.
>>   /V\       L   I   N   U   X
>>  // \\          I S    T H E
>>  /(   )\           W A Y
>>  ^^-^^
>>  cell phone :  +393473426510       e.mail:  [hidden email]
>>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


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Re: Again about the nasal cavity reconstruction

pieper
Administrator
Hi Samuele -

Glad to see the model is looking good - you can save in either .vtk or
.stl using the File->Save... option.

http://www.slicer.org/slicerWiki/index.php/Modules:Saving-Documentation-3.6

Best,
Steve


On 10/16/2010 05:21 PM, Samuele Zampini wrote:

> One more question about reconstructing the nasal cavity.
> I finally got the model in the picture. It is neither complete
> nor perfect, but I'd like to work on it.
>
> I got this model using the VMTKEasyLevelSetSegmentation.
> But how can I save a .vtk/.stl model?
>
> Thanks a lot,
>
> Samuele
>
>
>
> On Sat, Oct 16, 2010 at 5:44 PM, Sammy <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear Daniel,
>
>     sorry if I am writing again, but I can't succeed in doing a good
>     reconstruction.
>     I will now try to follow Ron's advice..
>
>     But have a look at what happens when I follow yours.
>
>     I get what you can see in the image attached.
>
>     How can I avoid to select the "outside volume"?
>
>     Thanks for your help,
>
>     Samuele
>
>
>
>
>     On Sat, Oct 16, 2010 at 3:46 PM, Daniel Haehn <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Please try the VMTKEasyLevelSetSegmentation instead the old,
>         deprecated
>         VMTKLevelSetSegmentation.
>
>         There is also a bunch of documentation on the wiki.
>
>         HTH,
>         Daniel
>
>         On Sat, 16 Oct 2010 14:33:22 +0200, Sammy
>         <[hidden email] <mailto:[hidden email]>>
>         wrote:
>          >>
>          >>
>          >> On Sat, Oct 16, 2010 at 1:25 PM, Daniel Haehn
>          > <[hidden email] <mailto:[hidden email]>>wrote:
>          >>
>          >>> Samuele,
>          >>>
>          >>> for VMTKEasyLevelSetSegmentation, the geometry does not
>         matter. You can
>          >>> name it as "region growing starting from a point". There is
>         no shape
>          >>> recognition like in VMTKVesselEnhancement.
>          >>>
>          >>
>          > There is something strange in the results I get. Please,
>         referring to the
>          > image attached,
>          > I'll ask you some questions:
>          > 1. the first question is about the initialization: I think
>         that the
>          > "colliding fronts" is the
>          > right choice.
>          > 2. about the Source Point, I chose the red one in the picture.
>          > 3. for the Target point, actually, I would need 2 points
>         (i.e. the 2
>          > nostrils). Can't I
>          > set 2 target points?
>          > 3. About the upper and lower threshold values, I think that
>         choosing
>          > -1000 and -500 is a good choice. The point is that as soon as
>         I set these
>          > 2
>          > values, everything becomes black.
>          >
>          > Any other advice?
>          >
>          >
>          >>
>          >> Now I'll try to follow your advice.
>          >> Thanks
>          >>
>          >>
>          >>>
>          >>> Daniel
>          >>>
>          >>> On Sat, 16 Oct 2010 10:44:33 +0200, Sammy
>         <[hidden email] <mailto:[hidden email]>>
>          >>> wrote:
>          >>> > On Fri, Oct 15, 2010 at 8:59 PM, Daniel Haehn
>         <[hidden email] <mailto:[hidden email]>>
>          >>> > wrote:
>          >>> >
>          >>> >> Hi Samuele,
>          >>> >>
>          >>> >> another approach would be to use the
>         VMTKEasyLevelSetSegmentation
>          >>> > module.
>          >>> >>
>          >>> >
>          >>> > I will try, even tough, AFAIK, VMTK features work well
>         when you have
>          > a
>          >>> > vessel-like
>          >>> > geometry. I think that the nasal-cavity is too complex.
>         But Ill try.
>          >>> >
>          >>> > Thanks,
>          >>> >
>          >>> > Samuele
>          >>> >
>          >>> >
>          >>> >>
>          >>> >> You can specify the right threshold for the air, you want to
>          > segment.
>          >>> > F.e.
>          >>> >> use source seeds which are the starting points of the front
>          > propagation
>          >>> > and
>          >>> >> target seeds where the propagation will stop. Just play
>         around a
>          > little
>          >>> > bit.
>          >>> >>
>          >>> >> HTH,
>          >>> >> Daniel
>          >>> >>
>          >>> >> On Oct 15, 2010, at 12:30 PM, Sammy wrote:
>          >>> >>
>          >>> >> > Dear all,
>          >>> >> >
>          >>> >> > I am still fighting against the nasal cavity
>         reconstruction. The
>          >>> point
>          >>> > is
>          >>> >> that I
>          >>> >> > tried to follow both your advice and the tutorials,
>         but I can not
>          > do
>          >>> >> everything
>          >>> >> > as I would like to.
>          >>> >> >
>          >>> >> > The first question is: to select only the air into the
>         nasal
>          > cavity,
>          >>> I
>          >>> >> placed a plane
>          >>> >> > at the inlet of the airflows (where there are the
>         nostrils - fig.
>          >>> >> inlet.png) and another
>          >>> >> >  one at the outlet of the trachea (not sure that is
>         the trachea,
>          >>> > sorry!,
>          >>> >> > fig. outlet.png)..
>          >>> >> >
>          >>> >> > Later, and that's the second question, what I would
>         like to do is
>          > to
>          >>> >> select the air
>          >>> >> > between these 2 planes (that's to say the inside of
>         the nasal
>          >>> > cavity!).
>          >>> >> > Which is the right feature that allows me to get the
>         result I am
>          >>> > looking
>          >>> >> for??
>          >>> >> > Is a button shown in the pictures attached or it
>         belongs to
>          > another
>          >>> >> module?
>          >>> >> > The reason I can not succeed in doing this operation
>         is that I try
>          >>> > with a
>          >>> >> > threshold, but it let me select the whole black
>         volume, not only
>          > the
>          >>> >> inside of
>          >>> >> > the nasal cavity, between the 2 "planes" I fixed!
>          >>> >> >
>          >>> >> > Also, about the "air": I think there's a filter that
>         helps to
>          > select
>          >>> > the
>          >>> >> black-volume,
>          >>> >> > i.e. the air. Could you let me know its name?
>          >>> >> >
>          >>> >> > Hope you can help,
>          >>> >> >
>          >>> >> > thanks in advance,
>          >>> >> >
>          >>> >> >
>          >>> >> > --
>          >>> >> >
>          >>> >>                                Samuele
>          >>> >> >
>          >
>         ____________________________________________________________________
>          >>> >> >
>          >>> >> >   .~.
>          >>> >> >   /V\       L   I   N   U   X
>          >>> >> >  // \\          I S    T H E
>          >>> >> >  /(   )\           W A Y
>          >>> >> >  ^^-^^
>          >>> >> >  cell phone :  +393473426510       e.mail:
>          >>> [hidden email] <mailto:[hidden email]>
>          >>> >> >  home        :   +390331823927       www:
>          >>> samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>          >>> >> >
>          >>> >> >
>          >>>
>         <inlet.png><outlet.png>_______________________________________________
>          >>> >> > slicer-users mailing list
>          >>> >> > [hidden email]
>         <mailto:[hidden email]>
>          >>> >> >
>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>          >>> >> > To unsubscribe: send email to
>          >>> >> [hidden email]
>         <mailto:[hidden email]> with
>         unsubscribe as
>          > the
>          >>> >> subject
>          >>> >>
>          >>> >>
>          >>> >
>          >>> >
>          >>> > --
>          >>> >
>          >>> >              Samuele Zampini
>          >>> >
>         ____________________________________________________________________
>          >>> >
>          >>> >   .~.
>          >>> >   /V\       L   I   N   U   X
>          >>> >  // \\          I S    T H E
>          >>> >  /(   )\           W A Y
>          >>> >  ^^-^^
>          >>> >  cell phone :  +393473426510       e.mail:
>         [hidden email] <mailto:[hidden email]>
>          >>> >  home        :   +390331823927       www:
>          > samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>          >>>
>          >>>
>          >>
>          >>
>          >> --
>          >>
>          >>              Samuele Zampini
>          >>
>         ____________________________________________________________________
>          >>
>          >>   .~.
>          >>   /V\       L   I   N   U   X
>          >>  // \\          I S    T H E
>          >>  /(   )\           W A Y
>          >>  ^^-^^
>          >>  cell phone :  +393473426510       e.mail:
>         [hidden email] <mailto:[hidden email]>
>          >>  home        :   +390331823927       www:
>         samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>          >>
>          >>
>          >
>          >
>          > --
>          >
>          >              Samuele Zampini
>          >
>         ____________________________________________________________________
>          >
>          >   .~.
>          >   /V\       L   I   N   U   X
>          >  // \\          I S    T H E
>          >  /(   )\           W A Y
>          >  ^^-^^
>          >  cell phone :  +393473426510       e.mail:
>         [hidden email] <mailto:[hidden email]>
>          >  home        :   +390331823927       www:
>         samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>
>
>
>
>     --
>
>                           Samuele Zampini
>     ____________________________________________________________________
>
>        .~.
>        /V\       L   I   N   U   X
>       // \\          I S    T H E
>       /(   )\           W A Y
>       ^^-^^
>       cell phone :  +393473426510       e.mail:
>     [hidden email] <mailto:[hidden email]>
>       home        :   +390331823927       www:
>     samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>
>
>
>
> --
>
>                   Samuele Zampini
> ____________________________________________________________________
>
>    .~.
>    /V\       L   I   N   U   X
>   // \\          I S    T H E
>   /(   )\           W A Y
>   ^^-^^
>   cell phone :  +393473426510       e.mail: [hidden email]
> <mailto:[hidden email]>
>   home        :   +390331823927       www: samiam1000.spaces.live.com
> <http://samiam1000.spaces.live.com>
>
>
>
> _______________________________________________
> 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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