Thread Subject: 3D reconstruction from 2D CT images

Hi,

I need to stack the 2D CT images, reconstruct them to 3D.

I need to segment the colon from the 2D CT images and reconstruct them to
view the inner surface of the colon.

Can somebody help me?

Thanks

"varulvel" <u40528@uwe> wrote in message
<7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and
reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

Try this package

http://hendrix.imm.dtu.dk/software/radon/code/Recon3D.tar.gz
and
http://hendrix.imm.dtu.dk/software/radon/code/Recon2D.tar.gz

Maybe you can find your solution.

Anh Huy Phan
RIKEN - BSI

In article <7df387e05dfa2@uwe>, varulvel <u40528@uwe> wrote:

>I need to stack the 2D CT images, reconstruct them to 3D.

Please do not repeat the same question several days in a row; it
is annoying, and will reach very few people who did not read the
question the first time.

--
   "Any sufficiently advanced bug is indistinguishable from a feature."
   -- Rich Kulawiec

Have you found a solution yet.If so, could you please share
how you got it. I am also trying to stack 2D CT images and
reconstruct a 3D image.

Thanks

"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and
reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

"varulvel" <u40528@uwe> wrote in message
<7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and
reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

I'll take a stab at this. Its an interesting problem. I
routinely construct 3D surfaces from 2D antenna gain
pattern data where the slices are basically a 2D contour.

Since you want to view the colon inner surface (and perhaps
the outer surface) I would likely try to accomplish this in
two parts.

I would try to extract the "inner" contour from each 2D CT
image and then griddata (or gridfit) the data onto a 3D
uniform cylindrical mesh of appropriate granularity created
using meshgrid. I would surface plot the gridded data and
allow the cylinder radius to distort with the data. You
might have to scale the radius data by trial and error a
few times until you get a meaningful image.

You could repeat this process for the outer contours and
then surface plot over the inner 3D shape. You can alter
the alpha (transparency) of the outer 3D shape so that it
does not obscure the inner colon image.

I like these medical imaging problems.

Scott

isosurface is your matlab function
... that you should apply to the stack i.e the ct volume
g






"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and
reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

hi..check this
http://www.nbb.cornell.edu/neurobio/land/PROJECTS/Reconstruction/index.html


"Gianni Schena" <schena@univ.trieste.it> wrote in message
<ft25va$8nb$1@fred.mathworks.com>...
>
>
> isosurface is your matlab function
> ... that you should apply to the stack i.e the ct volume
> g
>
>
>
>
>
>
> "varulvel" <u40528@uwe> wrote in message
<7df387e05dfa2@uwe>...
> > Hi,
> >
> > I need to stack the 2D CT images, reconstruct them to 3D.
> >
> > I need to segment the colon from the 2D CT images and
> reconstruct them to
> > view the inner surface of the colon.
> >
> > Can somebody help me?
> >
> > Thanks
> >
>

hi..check this
http://www.nbb.cornell.edu/neurobio/land/PROJECTS/Reconstruction/index.html


"Gianni Schena" <schena@univ.trieste.it> wrote in message
<ft25va$8nb$1@fred.mathworks.com>...
>
>
> isosurface is your matlab function
> ... that you should apply to the stack i.e the ct volume
> g
>
>
>
>
>
>
> "varulvel" <u40528@uwe> wrote in message
<7df387e05dfa2@uwe>...
> > Hi,
> >
> > I need to stack the 2D CT images, reconstruct them to 3D.
> >
> > I need to segment the colon from the 2D CT images and
> reconstruct them to
> > view the inner surface of the colon.
> >
> > Can somebody help me?
> >
> > Thanks
> >
>

hi ..check this
http://www.nbb.cornell.edu/neurobio/land/PROJECTS/Reconstruction/index.html

"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and
reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

Hello,

I have exacly the same question. Have you find a solution ?
I have 10 to 12 stacks of 2D images and would lke to reconstruct them in 3D.
Here a link with some images.

http://picasaweb.google.com/judith.hattab.mine/June17?authkey=3_bpe4Plvkc#

http://picasaweb.google.com/judith.hattab.mine/June24?authkey=wDYG7pCRCQw#

Thank you in advance,
Judith


"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>

Is this similar to what you are trying to do?

http://www.mathworks.com/access/helpdesk/help/techdoc/visualize/f5-3291.html


jiro

First, we need to clarify the question. Are you asking:

"I have 2D slices from a fully 3D CT dataset and I need to do something with them"

-OR-

"I have 2D image data which I wish to put together in order to create a 3D image"

??? Have a think, I'll presume the second answer in the meantime...

The originally posted question can be rephrased 'How different projections of an object be used to reconstruct it's 3D shape?.' This is the subject of tomography ('tomos' in greek is a 'section, slice or cutting' according to wikipedia!).

Now, there are a number of different types of tomography - my PhD is based around one, MART (Multiplicative Algebraic Reconstruction Technique) which I could help you to understand. However, I don't actually think that this is right for you. To my knowledge, Computerised Tomography (CT) for medical purposes is often done by means of a Radon Transform - one of the other posters gives a link to a radon transform site which might be useful.

Sorry, I don't know the details of radon transforms - but I can point you to exactly the right textbook to get you under way. The guru of the field is Gabor T Herman; check out one of his books:

Image Reconstruction from Projections: Fundamentals of Computed Tomography
G. T. Herman
Academic press 1981
ISBN-13: 978-0123420503

OR

Discrete Tomography: Foundations, Algorithms and Applications
G. T. Herman and A. Kuba
Birkhauser Verlag AG 1999
ISBN-13: 978-3764341015


... The latter is more up to date, so likely to be a bit more relevant for modern computing tasks. It's also cheaper.

Be warned that tomography can be incredibly computationally expensive. To give you an idea I've just bought a quad-core machine with 20Gb of ram to cope... although requirements vary wildly depending on the resolution you require, the number of elevations/sections you have, and the size of the 3D volume itself.

Hope this kicks you off...

Tom Clark

Hi
- can you suggesta reference for an introduction to M ART ?
- I'd like to evaluate reduced-view CT , should I also start with Herman and Kuba ?
- any suggested CT course/ppt's that include MATLAB excercises/samples ?

Thx,
AlexC

"Thomas Clark" <t.clark@remove.spamcantab.net> wrote in message <gh3289$o32$1@fred.mathworks.com>...
> First, we need to clarify the question. Are you asking:
>
> "I have 2D slices from a fully 3D CT dataset and I need to do something with them"
>
> -OR-
>
> "I have 2D image data which I wish to put together in order to create a 3D image"
>
> ??? Have a think, I'll presume the second answer in the meantime...
>
> The originally posted question can be rephrased 'How different projections of an object be used to reconstruct it's 3D shape?.' This is the subject of tomography ('tomos' in greek is a 'section, slice or cutting' according to wikipedia!).
>
> Now, there are a number of different types of tomography - my PhD is based around one, MART (Multiplicative Algebraic Reconstruction Technique) which I could help you to understand. However, I don't actually think that this is right for you. To my knowledge, Computerised Tomography (CT) for medical purposes is often done by means of a Radon Transform - one of the other posters gives a link to a radon transform site which might be useful.
>
> Sorry, I don't know the details of radon transforms - but I can point you to exactly the right textbook to get you under way. The guru of the field is Gabor T Herman; check out one of his books:
>
> Image Reconstruction from Projections: Fundamentals of Computed Tomography
> G. T. Herman
> Academic press 1981
> ISBN-13: 978-0123420503
>
> OR
>
> Discrete Tomography: Foundations, Algorithms and Applications
> G. T. Herman and A. Kuba
> Birkhauser Verlag AG 1999
> ISBN-13: 978-3764341015
>
>
> ... The latter is more up to date, so likely to be a bit more relevant for modern computing tasks. It's also cheaper.
>
> Be warned that tomography can be incredibly computationally expensive. To give you an idea I've just bought a quad-core machine with 20Gb of ram to cope... although requirements vary wildly depending on the resolution you require, the number of elevations/sections you have, and the size of the 3D volume itself.
>
> Hope this kicks you off...
>
> Tom Clark

"varulvel" <u40528@uwe> wrote in message <7df387e05dfa2@uwe>...
> Hi,
>
> I need to stack the 2D CT images, reconstruct them to 3D.
>
> I need to segment the colon from the 2D CT images and reconstruct them to
> view the inner surface of the colon.
>
> Can somebody help me?
>
> Thanks
>
sliceomatic.m has worked for me in the past - if your colon is easily seperated (eg it is the only material in a specific range of intensities)then it has controls to only show what you want. http://www.mathworks.com/matlabcentral/fileexchange/764

Alex,

I imagine that MART approaches are in Herman and Lent; but for a concise and simple application, look at:

Tomographic particle image velocimetry
G. E. Elsinga F. Scarano B. Wieneke B. W. van Oudheusden
Exp Fluids (2006) 41:933–947

... Ignore the bit about particle image velocimetry; just think of the particles as some object in the volume. This paper gives a really concise and simple explanation of MART.

- I'm sorry, I don't use CT type tomography in anger (always MART based tomo for me) so I don't know what reduced view CT is. Herman (and Kuba) have several books, including one on advanced techniques (which is really quite mathematical). Recommend you log on to amazon, and see whether you can browse the contents of any of them....

- I haven't come across any CT stuff in MATLAB; *BUT* I haven't searched for it at all. You might find an M-file on the FEX which'll implement a Radon Transform for you.

Kind regards

Tom Clark

"Alex L Chalmers" <remove.this.achalmers@as-e.com> wrote in message <gh3pj3$kqg$1@fred.mathworks.com>...
> Hi
> - can you suggesta reference for an introduction to M ART ?
> - I'd like to evaluate reduced-view CT , should I also start with Herman and Kuba ?
> - any suggested CT course/ppt's that include MATLAB excercises/samples ?
>
> Thx,
> AlexC
>
> "Thomas Clark" <t.clark@remove.spamcantab.net> wrote in message <gh3289$o32$1@fred.mathworks.com>...
> > First, we need to clarify the question. Are you asking:
> >
> > "I have 2D slices from a fully 3D CT dataset and I need to do something with them"
> >
> > -OR-
> >
> > "I have 2D image data which I wish to put together in order to create a 3D image"
> >
> > ??? Have a think, I'll presume the second answer in the meantime...
> >
> > The originally posted question can be rephrased 'How different projections of an object be used to reconstruct it's 3D shape?.' This is the subject of tomography ('tomos' in greek is a 'section, slice or cutting' according to wikipedia!).
> >
> > Now, there are a number of different types of tomography - my PhD is based around one, MART (Multiplicative Algebraic Reconstruction Technique) which I could help you to understand. However, I don't actually think that this is right for you. To my knowledge, Computerised Tomography (CT) for medical purposes is often done by means of a Radon Transform - one of the other posters gives a link to a radon transform site which might be useful.
> >
> > Sorry, I don't know the details of radon transforms - but I can point you to exactly the right textbook to get you under way. The guru of the field is Gabor T Herman; check out one of his books:
> >
> > Image Reconstruction from Projections: Fundamentals of Computed Tomography
> > G. T. Herman
> > Academic press 1981
> > ISBN-13: 978-0123420503
> >
> > OR
> >
> > Discrete Tomography: Foundations, Algorithms and Applications
> > G. T. Herman and A. Kuba
> > Birkhauser Verlag AG 1999
> > ISBN-13: 978-3764341015
> >
> >
> > ... The latter is more up to date, so likely to be a bit more relevant for modern computing tasks. It's also cheaper.
> >
> > Be warned that tomography can be incredibly computationally expensive. To give you an idea I've just bought a quad-core machine with 20Gb of ram to cope... although requirements vary wildly depending on the resolution you require, the number of elevations/sections you have, and the size of the 3D volume itself.
> >
> > Hope this kicks you off...
> >
> > Tom Clark

"Alex L Chalmers" <remove.this.achalmers@as-e.com> wrote in message

> sliceomatic.m has worked for me in the past - if your colon is easily seperated (eg it is the only material in a specific range of intensities)then it has controls to only show what you want. http://www.mathworks.com/matlabcentral/fileexchange/764

Can you give me some help with sliceomatic.m ?
I'm trying to import some mri slices of the colon, dicom files, without success.