Get bones in 3D slicer

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Get bones in 3D slicer

frederic
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Re: Get bones in 3D slicer

Sylvain Jaume-4
Hello Fred,

If you have a CT scan, you will be able to get an accurate segmentation using the Editor module and the implicit segmentation icon. You need to set the range of Hounsfield values that correspond to the bone intensities. In case that does not produce a satisfying result, would you mind sending a screenshot of what you obtain with Slicer and what you obtain with the other software packages?  

Sylvain

On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:

Hi,
 
In other dicom viewer software, It's possible to view automatically a 3D bones model. In 3d slicer, from now, I am only able to get a 3d bone model using the threshold function. Because it a manual segmentation it's not as precise as what I got with others softare. Cause I am a newby in 3dSlicer, I sure I can do better . My goal: get a humerus model, a scapula model (a segemented 3d model of the shoulder)
 
Does anybody have an idea?
 
Any suggestion would be appreciate
 
Best regards
 
Fred
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Re: Get bones in 3D slicer

madanrao
Hello,

I am using Editor module (LevelTracing) of Slicer3 3.5 alpha to segment a tumor (Ca Lung, left upper lobe). I used vmtkslicermodule to extract the trachea and the nearby aortic arch. I would like to try implicit rectangle (?segmentation) to segment out either tumor or aorta.

Attached image gives initial idea of the models built.

AM Mohan Rao



On Mon, Feb 8, 2010 at 11:22 AM, Sylvain Jaume <[hidden email]> wrote:
Hello Fred,

If you have a CT scan, you will be able to get an accurate segmentation using the Editor module and the implicit segmentation icon. You need to set the range of Hounsfield values that correspond to the bone intensities. In case that does not produce a satisfying result, would you mind sending a screenshot of what you obtain with Slicer and what you obtain with the other software packages?  

Sylvain

On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:

Hi,
 
In other dicom viewer software, It's possible to view automatically a 3D bones model. In 3d slicer, from now, I am only able to get a 3d bone model using the threshold function. Because it a manual segmentation it's not as precise as what I got with others softare. Cause I am a newby in 3dSlicer, I sure I can do better . My goal: get a humerus model, a scapula model (a segemented 3d model of the shoulder)
 
Does anybody have an idea?
 
Any suggestion would be appreciate
 
Best regards
 
Fred
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caLung.png (143K) Download Attachment
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Re: Get bones in 3D slicer

Sylvain Jaume-2
Hello Madan,

You can use the 'implicit rectangle' icon and set a lower threshold
and a higher threshold. Then you click on one corner of your region of
interest and pull the mouse to the opposite corner. Note that this
manual segmentation is 2D, so you will need to do the same operation
in multiple slices.

HTH,
Sylvain

On Mon, Feb 8, 2010 at 10:11 AM, Madan Rao <[hidden email]> wrote:

> Hello,
>
> I am using Editor module (LevelTracing) of Slicer3 3.5 alpha to segment a
> tumor (Ca Lung, left upper lobe). I used vmtkslicermodule to extract the
> trachea and the nearby aortic arch. I would like to try implicit rectangle
> (?segmentation) to segment out either tumor or aorta.
>
> Attached image gives initial idea of the models built.
>
> AM Mohan Rao
>
>
>
> On Mon, Feb 8, 2010 at 11:22 AM, Sylvain Jaume <[hidden email]>
> wrote:
>>
>> Hello Fred,
>> If you have a CT scan, you will be able to get an accurate segmentation
>> using the Editor module and the implicit segmentation icon. You need to set
>> the range of Hounsfield values that correspond to the bone intensities. In
>> case that does not produce a satisfying result, would you mind sending a
>> screenshot of what you obtain with Slicer and what you obtain with the other
>> software packages?
>>
>> Sylvain
>> On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:
>>
>> Hi,
>>
>> In other dicom viewer software, It's possible to view automatically a 3D
>> bones model. In 3d slicer, from now, I am only able to get a 3d bone model
>> using the threshold function. Because it a manual segmentation it's not as
>> precise as what I got with others softare. Cause I am a newby in 3dSlicer, I
>> sure I can do better . My goal: get a humerus model, a scapula model (a
>> segemented 3d model of the shoulder)
>>
>> Does anybody have an idea?
>>
>> Any suggestion would be appreciate
>>
>> Best regards
>>
>> Fred
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> 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: Get bones in 3D slicer

swallace
In reply to this post by frederic
Hi Fred,

The Iowa FEMesh module might have some potential utility to your goals:

http://wiki.slicer.org/slicerWiki/index.php/Modules:IA_FEMesh-Documentation-3.4

Stuart

> Hi,
>
> In other dicom viewer software, It's possible to view automatically a 3D
> bones model. In 3d slicer, from now, I am only able to get a 3d bone model
> using the threshold function. Because it a manual segmentation it's not as
> precise as what I got with others softare. Cause I am a newby in 3dSlicer,
> I sure I can do better . My goal: get a humerus model, a scapula model (a
> segemented 3d model of the shoulder)
>
> Does anybody have an idea?
>
> Any suggestion would be appreciate
>
> Best regards
>
> Fred_______________________________________________
> 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: Get bones in 3D slicer

Sylvain Jaume-2
In reply to this post by Sylvain Jaume-4
Hi Fred,

The screenshots you sent me indicate that you use the Implicit
Rectangle over the entire slice. Is that correct? You can define
different 'boxes' using the Implicit Rectangle over different 2D
regions. Additionally you can change the label value, let's say label
= 1 for the clavicle and label = 2 for scapula. To apply touch-ups on
the segmentation results you can use the Paint tool (icon showing a
paintbrush) and set the radius down to 1 on the left panel. The Editor
module (by Steve Pieper) contains many interactive segmentation tools
that you will find very intuitive.

Regards,
Sylvain

On Tue, Feb 9, 2010 at 10:10 AM, Fred L <[hidden email]> wrote:

> Hi,
> I joint a document in which I describe the difference.Thanks for all support
> you have given to me.
> Fred
> ________________________________
> From: Sylvain Jaume
> To: Fred Louazel
> Subject: Re: [slicer-users] Get bones in 3D slicer
> Date: Mon, 8 Feb 2010 00:52:59 -0500
> CC: [hidden email]
>
> Hello Fred,
> If you have a CT scan, you will be able to get an accurate segmentation
> using the Editor module and the implicit segmentation icon. You need to set
> the range of Hounsfield values that correspond to the bone intensities. In
> case that does not produce a satisfying result, would you mind sending a
> screenshot of what you obtain with Slicer and what you obtain with the other
> software packages?
>
> Sylvain
> On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:
>
> Hi,
>
> In other dicom viewer software, It's possible to view automatically a 3D
> bones model. In 3d slicer, from now, I am only able to get a 3d bone model
> using the threshold function. Because it a manual segmentation it's not as
> precise as what I got with others softare. Cause I am a newby in 3dSlicer, I
> sure I can do better . My goal: get a humerus model, a scapula model (a
> segemented 3d model of the shoulder)
>
> Does anybody have an idea?
>
> Any suggestion would be appreciate
>
> Best regards
>
> Fred
>
> _______________________________________________
> 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
>
> ________________________________
> Windows® phone-your Windows stuff, on the go. See more.
_______________________________________________
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Re: Get bones in 3D slicer

Sylvain Jaume-2
Hi Fred,

You can do everything with Slicer. Just use these modules in this sequence:

1. Cast Image: select output type 'float'
2. Gaussian Blur
3. Gray Scale Model Maker: set the value to half the label value (e.g.
if label=3, set value=1.5)

Regards,
Sylvain

On Thu, Feb 11, 2010 at 1:07 AM, Fred <[hidden email]> wrote:

> Hi !
>
> I use different Editor tools to improve the segmentation. Like you affirme,
> I realy use implicit rectangle to segment but I use the threshold fonction
> only.
>
> Now I have to smooth each surface before the meshing step.
>
> Do you have any idea about how to smooth surface in 3dslicer or other
> software ?
>
> Thank you very much for your help, all things setup very quickly because of
> you
>
> Best regards
>
> Fred
>
> --------------------------------------------------
> From: "Sylvain Jaume" <[hidden email]>
> Sent: Tuesday, February 09, 2010 10:56 AM
> To: "Fred L" <[hidden email]>
> Cc: <[hidden email]>
> Subject: Re: [slicer-users] Get bones in 3D slicer
>
>> Hi Fred,
>>
>> The screenshots you sent me indicate that you use the Implicit
>> Rectangle over the entire slice. Is that correct? You can define
>> different 'boxes' using the Implicit Rectangle over different 2D
>> regions. Additionally you can change the label value, let's say label
>> = 1 for the clavicle and label = 2 for scapula. To apply touch-ups on
>> the segmentation results you can use the Paint tool (icon showing a
>> paintbrush) and set the radius down to 1 on the left panel. The Editor
>> module (by Steve Pieper) contains many interactive segmentation tools
>> that you will find very intuitive.
>>
>> Regards,
>> Sylvain
>>
>> On Tue, Feb 9, 2010 at 10:10 AM, Fred L <[hidden email]> wrote:
>>>
>>> Hi,
>>> I joint a document in which I describe the difference.Thanks for all
>>> support
>>> you have given to me.
>>> Fred
>>> ________________________________
>>> From: Sylvain Jaume
>>> To: Fred Louazel
>>> Subject: Re: [slicer-users] Get bones in 3D slicer
>>> Date: Mon, 8 Feb 2010 00:52:59 -0500
>>> CC: [hidden email]
>>>
>>> Hello Fred,
>>> If you have a CT scan, you will be able to get an accurate segmentation
>>> using the Editor module and the implicit segmentation icon. You need to
>>> set
>>> the range of Hounsfield values that correspond to the bone intensities.
>>> In
>>> case that does not produce a satisfying result, would you mind sending a
>>> screenshot of what you obtain with Slicer and what you obtain with the
>>> other
>>> software packages?
>>>
>>> Sylvain
>>> On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> In other dicom viewer software, It's possible to view automatically a 3D
>>> bones model. In 3d slicer, from now, I am only able to get a 3d bone
>>> model
>>> using the threshold function. Because it a manual segmentation it's not
>>> as
>>> precise as what I got with others softare. Cause I am a newby in
>>> 3dSlicer, I
>>> sure I can do better . My goal: get a humerus model, a scapula model (a
>>> segemented 3d model of the shoulder)
>>>
>>> Does anybody have an idea?
>>>
>>> Any suggestion would be appreciate
>>>
>>> Best regards
>>>
>>> Fred
>>>
>>> _______________________________________________
>>> 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
>>>
>>> ________________________________
>>> Windows® phone-your Windows stuff, on the go. See more.
>
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Re: Get bones in 3D slicer

Sylvain Jaume-2
Hi Fred,

I CC slicer-users on this email as other users may benefit from it.
Please write in English...

To use the GaussianBlur module, you need to set the Input Volume to
the results of CastImage and to set the Output Volume to 'Create New
Volume'. You can leave Sigma (standard deviation) to its default value
1.

Let me know if you have any issue.
Sylvain

On Sat, Feb 13, 2010 at 11:49 AM, Fred <[hidden email]> wrote:

> Salut Sylvain,
>
> J'ai débuté le lissage de mes volumes. Le module cast fonctionne. Lorsque
> j'arrive dans le module guassian blur, j'entre le label dessiné précédemment
> avec implicite rectangle. Je laisse la valeur sigma a 1 , car je ne sais pas
> à quoi elle sert. Le module roule, mais "avec erreur" et je ne peux pas
> sauvegarder le volume résultant. Tu sembles avoir une longue expérience.
> As-tu une idée qui explique ça ?
>
> Un gros merci
>
> Fred

On Thu, Feb 11, 2010 at 1:40 AM, Sylvain Jaume <[hidden email]> wrote:

> Hi Fred,
>
> You can do everything with Slicer. Just use these modules in this sequence:
>
> 1. Cast Image: select output type 'float'
> 2. Gaussian Blur
> 3. Gray Scale Model Maker: set the value to half the label value (e.g.
> if label=3, set value=1.5)
>
> Regards,
> Sylvain
>
> On Thu, Feb 11, 2010 at 1:07 AM, Fred <[hidden email]> wrote:
>> Hi !
>>
>> I use different Editor tools to improve the segmentation. Like you affirme,
>> I realy use implicit rectangle to segment but I use the threshold fonction
>> only.
>>
>> Now I have to smooth each surface before the meshing step.
>>
>> Do you have any idea about how to smooth surface in 3dslicer or other
>> software ?
>>
>> Thank you very much for your help, all things setup very quickly because of
>> you
>>
>> Best regards
>>
>> Fred
>>
>> --------------------------------------------------
>> From: "Sylvain Jaume" <[hidden email]>
>> Sent: Tuesday, February 09, 2010 10:56 AM
>> To: "Fred L" <[hidden email]>
>> Cc: <[hidden email]>
>> Subject: Re: [slicer-users] Get bones in 3D slicer
>>
>>> Hi Fred,
>>>
>>> The screenshots you sent me indicate that you use the Implicit
>>> Rectangle over the entire slice. Is that correct? You can define
>>> different 'boxes' using the Implicit Rectangle over different 2D
>>> regions. Additionally you can change the label value, let's say label
>>> = 1 for the clavicle and label = 2 for scapula. To apply touch-ups on
>>> the segmentation results you can use the Paint tool (icon showing a
>>> paintbrush) and set the radius down to 1 on the left panel. The Editor
>>> module (by Steve Pieper) contains many interactive segmentation tools
>>> that you will find very intuitive.
>>>
>>> Regards,
>>> Sylvain
>>>
>>> On Tue, Feb 9, 2010 at 10:10 AM, Fred L <[hidden email]> wrote:
>>>>
>>>> Hi,
>>>> I joint a document in which I describe the difference.Thanks for all
>>>> support
>>>> you have given to me.
>>>> Fred
>>>> ________________________________
>>>> From: Sylvain Jaume
>>>> To: Fred Louazel
>>>> Subject: Re: [slicer-users] Get bones in 3D slicer
>>>> Date: Mon, 8 Feb 2010 00:52:59 -0500
>>>> CC: [hidden email]
>>>>
>>>> Hello Fred,
>>>> If you have a CT scan, you will be able to get an accurate segmentation
>>>> using the Editor module and the implicit segmentation icon. You need to
>>>> set
>>>> the range of Hounsfield values that correspond to the bone intensities.
>>>> In
>>>> case that does not produce a satisfying result, would you mind sending a
>>>> screenshot of what you obtain with Slicer and what you obtain with the
>>>> other
>>>> software packages?
>>>>
>>>> Sylvain
>>>> On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:
>>>>
>>>> Hi,
>>>>
>>>> In other dicom viewer software, It's possible to view automatically a 3D
>>>> bones model. In 3d slicer, from now, I am only able to get a 3d bone
>>>> model
>>>> using the threshold function. Because it a manual segmentation it's not
>>>> as
>>>> precise as what I got with others softare. Cause I am a newby in
>>>> 3dSlicer, I
>>>> sure I can do better . My goal: get a humerus model, a scapula model (a
>>>> segemented 3d model of the shoulder)
>>>>
>>>> Does anybody have an idea?
>>>>
>>>> Any suggestion would be appreciate
>>>>
>>>> Best regards
>>>>
>>>> Fred
>>>>
>>>> _______________________________________________
>>>> 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
>>>>
>>>> ________________________________
>>>> Windows® phone-your Windows stuff, on the go. See more.
>>
>
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Re: Get bones in 3D slicer

madanrao
Hello all,

Fred's query is translated by my daughter (a high school student):

I started the smoothing of my volumes. Module cast works. When
I arrive in module to guassian blur, I enter the quality-label drawn before
with implicit right-angled. I leave the value sigma has 1, because I do not know
for what it serves. Module runs, but " with error " and I cannot
safeguard the resultant volume. You seem to have a long experience.
Have you an idea which explains this?

A.M.Mohan Rao

On Sat, Feb 13, 2010 at 11:06 PM, Sylvain Jaume <[hidden email]> wrote:
Hi Fred,

I CC slicer-users on this email as other users may benefit from it.
Please write in English...

To use the GaussianBlur module, you need to set the Input Volume to
the results of CastImage and to set the Output Volume to 'Create New
Volume'. You can leave Sigma (standard deviation) to its default value
1.

Let me know if you have any issue.
Sylvain

On Sat, Feb 13, 2010 at 11:49 AM, Fred <[hidden email]> wrote:
> Salut Sylvain,
>
> J'ai débuté le lissage de mes volumes. Le module cast fonctionne. Lorsque
> j'arrive dans le module guassian blur, j'entre le label dessiné précédemment
> avec implicite rectangle. Je laisse la valeur sigma a 1 , car je ne sais pas
> à quoi elle sert. Le module roule, mais "avec erreur" et je ne peux pas
> sauvegarder le volume résultant. Tu sembles avoir une longue expérience.
> As-tu une idée qui explique ça ?
>
> Un gros merci
>
> Fred

On Thu, Feb 11, 2010 at 1:40 AM, Sylvain Jaume <[hidden email]> wrote:
> Hi Fred,
>
> You can do everything with Slicer. Just use these modules in this sequence:
>
> 1. Cast Image: select output type 'float'
> 2. Gaussian Blur
> 3. Gray Scale Model Maker: set the value to half the label value (e.g.
> if label=3, set value=1.5)
>
> Regards,
> Sylvain
>
> On Thu, Feb 11, 2010 at 1:07 AM, Fred <[hidden email]> wrote:
>> Hi !
>>
>> I use different Editor tools to improve the segmentation. Like you affirme,
>> I realy use implicit rectangle to segment but I use the threshold fonction
>> only.
>>
>> Now I have to smooth each surface before the meshing step.
>>
>> Do you have any idea about how to smooth surface in 3dslicer or other
>> software ?
>>
>> Thank you very much for your help, all things setup very quickly because of
>> you
>>
>> Best regards
>>
>> Fred
>>
>> --------------------------------------------------
>> From: "Sylvain Jaume" <[hidden email]>
>> Sent: Tuesday, February 09, 2010 10:56 AM
>> To: "Fred L" <[hidden email]>
>> Cc: <[hidden email]>
>> Subject: Re: [slicer-users] Get bones in 3D slicer
>>
>>> Hi Fred,
>>>
>>> The screenshots you sent me indicate that you use the Implicit
>>> Rectangle over the entire slice. Is that correct? You can define
>>> different 'boxes' using the Implicit Rectangle over different 2D
>>> regions. Additionally you can change the label value, let's say label
>>> = 1 for the clavicle and label = 2 for scapula. To apply touch-ups on
>>> the segmentation results you can use the Paint tool (icon showing a
>>> paintbrush) and set the radius down to 1 on the left panel. The Editor
>>> module (by Steve Pieper) contains many interactive segmentation tools
>>> that you will find very intuitive.
>>>
>>> Regards,
>>> Sylvain
>>>
>>> On Tue, Feb 9, 2010 at 10:10 AM, Fred L <[hidden email]> wrote:
>>>>
>>>> Hi,
>>>> I joint a document in which I describe the difference.Thanks for all
>>>> support
>>>> you have given to me.
>>>> Fred
>>>> ________________________________
>>>> From: Sylvain Jaume
>>>> To: Fred Louazel
>>>> Subject: Re: [slicer-users] Get bones in 3D slicer
>>>> Date: Mon, 8 Feb 2010 00:52:59 -0500
>>>> CC: [hidden email]
>>>>
>>>> Hello Fred,
>>>> If you have a CT scan, you will be able to get an accurate segmentation
>>>> using the Editor module and the implicit segmentation icon. You need to
>>>> set
>>>> the range of Hounsfield values that correspond to the bone intensities.
>>>> In
>>>> case that does not produce a satisfying result, would you mind sending a
>>>> screenshot of what you obtain with Slicer and what you obtain with the
>>>> other
>>>> software packages?
>>>>
>>>> Sylvain
>>>> On Feb 7, 2010, at 11:41 PM, "Fred" <[hidden email]> wrote:
>>>>
>>>> Hi,
>>>>
>>>> In other dicom viewer software, It's possible to view automatically a 3D
>>>> bones model. In 3d slicer, from now, I am only able to get a 3d bone
>>>> model
>>>> using the threshold function. Because it a manual segmentation it's not
>>>> as
>>>> precise as what I got with others softare. Cause I am a newby in
>>>> 3dSlicer, I
>>>> sure I can do better . My goal: get a humerus model, a scapula model (a
>>>> segemented 3d model of the shoulder)
>>>>
>>>> Does anybody have an idea?
>>>>
>>>> Any suggestion would be appreciate
>>>>
>>>> Best regards
>>>>
>>>> Fred
>>>>
>>>> _______________________________________________
>>>> 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
>>>>
>>>> ________________________________
>>>> Windows® phone-your Windows stuff, on the go. See more.
>>
>
_______________________________________________
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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[hidden email]
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