Hi Luca,
thanks for your prompt response.
I guess I understood what you suggested. I also tried to run the code you
attached, but without results.
Now I have three images (name them CCA.vti, ICA.vti, ECA.vti) yielded by
vmtksurfacemodeller. These different images doesn't have the same origin,
but have the same spacing. To better explain what is my difficulty in
solving this problem, I could say that you can imagine the different images
located as follows:
CCA.vti has origin [350.79, 2.69, 9.60] and dimension 65x68x198;
ICA.vti [358.33, 11.48, 49.40] and dimensions 26x31x40;
ECA.vti [351.97, 6.20 , 49.40] and dimensions 26x21x40.
When I reslice ICA.vti in CCA.vti, as you told me, I produce a new image
with dimensions 65x68x198, which is completely black either I put negative
value as background or a positive one. Now I see that two images to be
composed together should have the same origin and the same sample spacing.
So as an example, if I want to merge CCA.vti and ICA.vti, refering with the
dimensions above, both CCA.vti and ICA.vti should have dimensions
26x31x238, shouldn't they? If they should, how can I do it using
vmtkimagereslice?
I thank you in advance again.
Best Regards
2011/11/3 Luca Antiga <luca.ant...@orobix.com>
> Hi Giuseppe,
> I think the approach of lofting the three branches separately is the way
> to go.
>
> When you use vmtkimagecompose you have to make sure of a few things:
>
> - that the images you are trying to merge have the same number of pixels
> in each direction and have the same spacing and origin;
> - that you choose the right compose operation: if the images produced by
> vmtksurfacemodeller are positive inside the vessel, you should choose
> -operation max, otherwise -operation min.
>
> If your images have different number of pixels, origins or spacings, you
> need to resample one over the other before composing. Say you have
> image2.mha that you want to merge with image1.mha: run
> vmtkimagereslice -ifile image2.mha -rfile image1.mha -ofile image2on1.mha
> -background 4.0
> At this point image2on1.mha will be image2 resampled on image1's grid, so
> you can proceed and compose them. Note that the -background has to be set
> to a negative value if the vessel interior is positive, and positive if the
> vessel is negative.
>
> I hope you have enough information to get started.
>
> Best regards
>
> Luca
>
>
> On Nov 3, 2011, at 4:13 PM, Giuseppe Isu wrote:
>
> > Hello everybody,
> >
> > I'm dealing with a reconstruction of two stenosesd carotid bifurcations
> by DICOM sets of MRI black-blood images.
> > Since I couldn't perform level set segmentation by vmtk due to the
> black-blood images, and since negating images entails a loss of information
> in the stenosed area (stenosis became hard to disitinguish), I used a
> commercial software for segmentation and I obtained a set of polylines.
> >
> > Doing this, the first problem encountered has been lofting the surfaces
> over the curves: at the bifurcation site lofting becomes impractical and I
> could only loft CCA, ICA and ECA surfaces separately. I thought of using
> vmtk to solve this problem and in particular I thought of
> vmtksurfacemodeller script.
> > My idea was to input this script the entire *.stl geometry (of CCA, ICA
> and ECA surfaces unlinked to each other), yielding a vti image and then
> performing marching cubes.
> > This procedure succeeded for one of my carotids, and I tried to perform
> the same sequence of comands also for a second carotid geometry that I need
> to reconstruct. This time whithout any result: the vti image returned by
> vmtksurfacemodeller is quitely noisy (I figure out it's due to
> miscalculation of distance function near the bifurcation site).
> > Nevertheless I didn't give up! I thought of a second possible solution
> that implies the use of vmtksurfacemodeller but in a different way.
> > I extracted separately vti images of respectively CCA, ICA and ECA
> branches and I thought to compose the image with the script
> vmtkimagecompose but without results.
> > Now I have three different images which I want to merge but I can't do
> this and I can't understand if it is a possible task or, otherwise, I ought
> to change approach.
> >
> > Could you help me?
> >
> > I thank you in advance
> >
> > --
> > Giuseppe Isu
> >
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>
--
Giuseppe
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