Issue defining aitch bone from leg bone

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Issue defining aitch bone from leg bone

AndyH
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Re: Issue defining aitch bone from leg bone

Murat Maga
If intensity difference between bone and other elements (cartilage and ligaments) is not sufficiently high for you to distinguish them using threshold effect, I am afraid your remaining option is to segment them manually using paint or other tools based on your anatomical insight.

M

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of AndyH
Sent: Monday, January 16, 2017 6:11 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Issue defining aitch bone from leg bone

I'm a new 3d Slicer user, currently analysing CT scans of a sheep's aitch bone in 3D slicer, however the carcass was scanned with the leg bones attached, and as such the aitch and leg bones appear fused together when I make my model (using the threshold effect). I originally thought that this was a result of having the lower threshold limit too low (hence showing cartilage and ligaments), but any attempts at increasing the lower limit results in some of the bone being removed.
I was wondering anybody had a means of making a model that won't appear fused together, as I'm somewhat at a loss on how to do this.



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Re: Issue defining aitch bone from leg bone

Csaba Pinter-2
You can use the Segment Editor module where you can threshold them separately using the Scissors effect (fill inside) and the threshold set as mask (that you can set in the Threshold effect then set as mask after approving the preview).

csaba

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: Monday, January 16, 2017 22:46
To: AndyH <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Issue defining aitch bone from leg bone

If intensity difference between bone and other elements (cartilage and ligaments) is not sufficiently high for you to distinguish them using threshold effect, I am afraid your remaining option is to segment them manually using paint or other tools based on your anatomical insight.

M

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of AndyH
Sent: Monday, January 16, 2017 6:11 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Issue defining aitch bone from leg bone

I'm a new 3d Slicer user, currently analysing CT scans of a sheep's aitch bone in 3D slicer, however the carcass was scanned with the leg bones attached, and as such the aitch and leg bones appear fused together when I make my model (using the threshold effect). I originally thought that this was a result of having the lower threshold limit too low (hence showing cartilage and ligaments), but any attempts at increasing the lower limit results in some of the bone being removed.
I was wondering anybody had a means of making a model that won't appear fused together, as I'm somewhat at a loss on how to do this.



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Re: Issue defining aitch bone from leg bone

AndyH
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Re: Issue defining aitch bone from leg bone

AndyH
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Re: Issue defining aitch bone from leg bone

Delvan Neville
In reply to this post by AndyH
You can try the GrowCut tool for that as a middle ground rather than manually segmenting each slice by hand.  Use the Paint tool to mark the portions of a few example slices of what is ligament, what is cartilage, what is the aitch bone, etc.  You'll find a tutorial for it on the wiki.  However if your CT doesn't have good contrast between bone and ligaments where they connect to the bone, GrowCut might not be able to discern where the ligament ends and the bone begins.

You could also manually segment the ligament in the slices where they end up overlapping in thresholding with the bone, then using the Masking feature to only allow thresholding outside of existing segments.

Sincerely,
Delvan Neville

On Tue, Jan 17, 2017 at 12:56 PM, AndyH <[hidden email]> wrote:
Is there no way to refine CT Image scans before modelling and segmenting, so
that 3d slicer can tell the difference between the bones before any
modelling is done? Or where I can somehow define where I believe the
beginning and end points (on a 2d slice) of the socket joint are, that 3d
slicer can then essentially grow those lines to form the ball and socket
joint, hence separating the bones?
My study is on the socket joint, hence simply painting on the gap really
defeats the purpose of my study.



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Re: Issue defining aitch bone from leg bone

Andras Lasso-2

If there is no contrast difference at all then you can use geometric interpolation: you create complete segmentation on a couple of slices and Slicer computes contours on slices between them. It may save you some time.

 

Both image-based geometric interpolation methods are available in the Segment Editor module, in Auto-complete effect. Use “Grow from seeds” method if there is some contrast between different structures. Use “Fill between parallel slices” method if there is no sufficient contrast and you can only delineate structures based on your knowledge of anatomy.

 

See instructions about how to use Auto-complete effect here:

https://lassoan.gitbooks.io/test-book/content/modules/segment-editor/

 

Andras

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Delvan Neville
Sent: January 17, 2017 16:07
To: AndyH <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Issue defining aitch bone from leg bone

 

You can try the GrowCut tool for that as a middle ground rather than manually segmenting each slice by hand.  Use the Paint tool to mark the portions of a few example slices of what is ligament, what is cartilage, what is the aitch bone, etc.  You'll find a tutorial for it on the wiki.  However if your CT doesn't have good contrast between bone and ligaments where they connect to the bone, GrowCut might not be able to discern where the ligament ends and the bone begins.

 

You could also manually segment the ligament in the slices where they end up overlapping in thresholding with the bone, then using the Masking feature to only allow thresholding outside of existing segments.


Sincerely,
Delvan Neville

 

On Tue, Jan 17, 2017 at 12:56 PM, AndyH <[hidden email]> wrote:

Is there no way to refine CT Image scans before modelling and segmenting, so
that 3d slicer can tell the difference between the bones before any
modelling is done? Or where I can somehow define where I believe the
beginning and end points (on a 2d slice) of the socket joint are, that 3d
slicer can then essentially grow those lines to form the ball and socket
joint, hence separating the bones?
My study is on the socket joint, hence simply painting on the gap really
defeats the purpose of my study.



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Re: Issue defining aitch bone from leg bone

AndyH
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Re: Issue defining aitch bone from leg bone

AndyH
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Re: Issue defining aitch bone from leg bone

Andras Lasso-2
In reply to this post by AndyH
The Auto-complete effect is in Segment Editor module (not in the old Editor module).

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of AndyH
Sent: January 17, 2017 20:35
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Issue defining aitch bone from leg bone

I can find neither the Auto-complete effect, nor the Grow From Seeds effect.
Could you point me in the right direction here? I thought they might be in the 4.7 Nightly build, so I downloaded that (because I only had 4.2), but there is still no sign of it.



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