Dear All,
I am using AVIZO to reconstruct 3D from CT-Scan images. There are two types of images that I have (form different CT machines). First series are created by having slices in 3 directions (X, Y, Z) and I can easily reconstruct them in AVIZO. But there is a second type, in which images are created by rotating the specimen inside the CT machine while scanning (360 degrees). When I load this type of images in AVIZO, instead of having a spherical shape for example, I end up having a cylindrical shape. And the reason is, AVIZO puts these slices in one direction instead of reading them in rotating order.
Does anybody know how I can load this type of images?
With all thanks,
Arsalan
Hello dear;
I have not worked with AVIZO software but I use MATLAB for 3D data analysis. I suggest you use MATLAB because MATLAB is more practical and wider.
Good luck
Dear Mohammad,
Thanks for recommending Matlab :-)
Unfortunately, I don't have time to learn Matlab but what I noticed is that these images needed to be reconstructed using the software which usually comes with that CTscan machine.
Thanks again,
Arsalan
Hello dear Mr Arsalan
By googling, you will find many codes for image reconstruction using matlab. For example:
https://www.mathworks.com/matlabcentral/fileexchange/34608-ct-reconstruction-package
Best regards
M Rezaei
Saeid Hosseini
Dear Saeid,
Are these all images that you have? I think your images should be in same distance. When I look at your axial image, it seems that images are in different distances (0.05, 0.07, 0.1). If you have the dicom file for these it would be easy, just load it in Avizo and work on what you want. Otherwise (with current images), if possible, it may be a bit tricky!
Best,
Arsalan
Hi dear Arsalan Marghoub,
It looks like you are trying to load a stack of projection images. Avizo will always open the images stacking them one over each other. This is will work for seeing the projection (the images that are taken originally in a CT scanner). If you open them stacked one over each other, they will look more or less like a sinogram, when looking in a 3D render in a side view.
If you really want to look at the projections, try using ImageJ. It will load all of them in a sequence, and you will be able to see one by one.
Best,
Liebert
Liebert Parreiras Nogueira
Thanks dear Liebert,
I'll try ImageJ, maybe some day!
Hi there,
What you need to do is reconstruction followed by slicing. After that you will have stack of images with equal spacing. Check this blog post.
https://peterfalkingham.com/2019/02/18/free-software-for-ct-segmentation-2019/
Nasseh Khodaie Hi there!
Thanks for sharing the blog post.
I have no problem with reconstructed images as I am familiar with a plenty of software packages that can handle the segmentation.
My main problem is when CT images are passed to me without initial reconstruction which should normally be done right after scanning!
I guess I need to figure out how to do this in Matlab :-p