The first step to diagnose your performance problem is a good benchmark to get the following information along every step of your processing:

• Memory usage
• CPU usage (pay attention to the number of cores that are used and at what percentage)
• Loading image time (maybe a SSD could help if your performance is IO bounded)

The first thing that comes to my mind is that your are using Matlab for "production" intensive processing. This kind of heavy computation is generally done in C or C++, at least based on such libraries like OpenCV, and often send to GPU for even more performance.  Using Matlab, you have almost no control on how to parallelize the work or send some of it to GPU.

This being said, you also have to pay attention to data locality.  You have such huge data sets that if your data structures and access patterns are not cache-friendly, you can be kill by cache miss. Again, a good benchmarking tool can help you diagnose this but I don't know if Matlab can do this.  Again, C/C++ are better than Matlab to fine tune this kind of things.

I can't repeat enough the need to get good benchmark scaffolding in place before you start poking into your system. You might even find quick wins even in Mathlab without using new hardware.

Good luck, this is an interesting problem to investigate!

In the case of the commercially available solution COBRA from Exxim, we recommend 12 GB of RAM, i7 or Xeon CPU, and a CUDA-capable graphics card from NVidia with 2 GB of on-board RAM. This configuration has plenty of compute power for micro-CT. The speed of back-projection depends on the GPU, the speed of corrections on the CPU. We have not seen much influence of SSD versus conventional hard drives.

The specs that M. Bruning are suggesting are more in par with what I was expecting a good optimized software would need to do the job. Again, Matlab is good for prototyping but once your algorithm is fine tuned, production use should use an optimized software/library to work on lots of data.

Thanks very much for your answers so far. We are using a custom-made CT system with an own X-ray source at a Physics institute. Maybe that´s why  the RAM and graphics card requirements appear higher.

I think the kind of software used for reconstruction is also important. Our collaborators use Avizo 3D, but it would be great if you had other suggestions (e.g. Exxim).

Again, thank you very much for answering!

Best regards,

Christoph

As already mentionned above, you should benchmark what is used by the software in order to improve the performance. Actually, the big question is "does the software using the GPU or the CPU?". According the answer you might put 2 graphic cards in your computer, or a good CPU with 32 Gb of RAM and a SSD of 250 Gb.

1/ Now, by experience, memory can be a big issue 1) as you cannot have enough memory to put all the picture in the RAM, 2) the software can work with limited amount of memory but the process is slowdown as the software goes back and forth between the RAM and the hard drive.

2/ Some software use the GPU (the graphic card) so in this cas, that will be the memory and the graphic card the issue. A good 3Gb of RAM on the graphic card should put you out of trouble most of the case.

3/ In case of intense use of the hard drive because your files are too big for the memory, a SSD could dramatically improve your performance. Again 250 Gb should be enough.

I have a i7 with 16 Gb of RAM, GTX 960 with 4 GB and a 1Tb hard drive (not SSD). And everything is going well with reasonable computing time (from 20 min to several hours).

Wish you the best

Geoffrey

i highly advice you a builded workstation like the Dell Precission 7910  at max configuration

• dual xeon 18x2 cors at 2.4 GH
• 1TB of ram
• nvidia quadro 8GB
• 10 TB of SSD
• linux redhat or windows 10

http://configure.us.dell.com/dellstore/config.aspx?oc=cup7910w7p_4&model_id=precision-t7910-workstation&c=us&l=en&s=bsd&cs=04

you will gain high performance and no worry about compatibility between components 

is extramly expensive but for your kind of application and there future you need this kind of computer 

Thanks a lot, I am about to configure such a workstation right now. Very helpful!