CT Scanner hardware and data

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Sep 29, 2004
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I was wondering what kind of hardware is needed to view CT scans. How big are the data files? How much memory is occupied? What kind of CPU is needed?

This sort of thing.

Or is it less complex than I realize and a 5 year old laptop can do this?
 

Mark R

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Oct 9, 1999
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What sort of CT scans?

Medical, industrial?
Do you have image data files, or do you only have the raw data from the scanner that needs processing?
 
Sep 29, 2004
18,656
67
91
What sort of CT scans?

Medical, industrial?
Do you have image data files, or do you only have the raw data from the scanner that needs processing?

I was thinking medical. maybe a CT scan of a knee.

I'm mostly curious so I don't know how to answer images vs raw data. Should I assume that there is raw data and from that images are made that represent slices every X mm? And that a doctor in his office would be looking at the image data? I guess the answer is, if a doctor were looking at CT scan results on his PC, what data would he be using?

I am curious as to what data the doctor uses in his office. But if you know what kind of memory and CPU power is needed to view raw data and image data, that would be appreciated.
 

Mark R

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Oct 9, 1999
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OK. Medical CT scans are saved as images in a format called DICOM.

The raw data is usually proprietary and can only be processed by software on the scanner console, or a workstation with the scanner engine reconstruction engine software on it. This type of data would not be archived or transmitted anywhere as it's not useful. It might stay on the scanner hard drive for a bit, just incase the doc wants different image generation parameters tried.

DICOM is an open standard, but it's a bit obscure as it's only used in medical work. The image data is almost always saved as uncompressed pixel data (16 bit greyscale), but may be compressed with JPEG2000 or, if old, lossless JPEG. There is some open source software for viewing it available - by far the best OSS is Osirix for Mac OS X and iOS. There really isn't anything remotely comparable for windows or linux. Although, a doc would be using a commercial package (likely costing $2-5k per user per year) and these typically are very full featured.

CT scans are almost always acquired at 512x512 per image, giving an image file size of 528k (512 k pixel data + 16k header).

How many images in a scan varies depending on type of scan and scan tech/doc preference. Modern scanners have a voxel resolution of better 0.5 x 0.5 x 0.5 mm, and its increasingly common practice to produce an image for each 0.5 mm (or less) in the "z" direction.

This type of data set is almost like the scanner raw data - with the right software (and generic software, this time) you can combine images to simulate thicker "slices", or do other kinds of processing - change the plane of the slice, volume rendering, etc. In general, you need some sort of GPU to do this on the fly, but it doesn't need to be that beefy.

It's important to distinguish between "basic" software - which just loads 1 image at a time and shows it on screen, and allows you to "scroll" between images with the mouse; and "advanced" software which can reslice or 3D render (or do other types of processing, e.g. average multiple slices together to improve signal-to-noise ratio, but at the cost of resolution, etc.).

A few years ago, I knocked up a program in c# over a weekend to do this sort of advanced processing, and it ran fine on a 5750 - the volume rendering was a bit slow - maybe 5 fps with quadrilinear filtering - but not terrible. Screen shot here. In the screenshot the actual image, as saved, is shown at top right - the other images are generated by "stacking" the slice images and "re-slicing" in software.

For something like a knee CT, where the doc is interested in fine bone detail - it would be normal to have 300 or 400 0.5mm slice images - giving a total data size of about 200 MB. For convenience, in case the doc doesn't have advanced software, it may be common for the scanner to be set up to automatically "reslice" the images in pre-defined planes and save those images as well.

For something like a brain CT, where fine detail is not needed, but high signal-to-noise ratio is, then you might only have 30 images saved because they are "thick" 5 mm slices. However, the doc might also be interested in a skull fracture, so the might need the "thin" 0.5 mm images as well.

The latest technology is "dynamic" or 4D CT. Where entire CT volume scans are repeated at 1-2 fps. So, imagine a CT brain artery study (where fine detail is needed). 640 images @ 512x512 for 30 frames. You're in serious trouble trying to do anything with that (that's about 10 GB of data).

In terms of hardware, if you're not wanting to do 3D reslicing on whole-body 0.5 mm CT scans, then you don't really need much hardware.

I've set up a medical teleradiology system (used by radiologists for real medical diagnosis). The hardware is Ivy bridge Core i3, 4 GB RAM, Win 7 and 2x Dell U2713H + spyder calibrator. The ivy bridge GPU is plenty fast enough for real-time reslicing and 3D rendering.
 

jaedaliu

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Feb 25, 2005
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Based on my experience with MRI, not much.

I have 2 different CDs with my MRIs from 2 different EMR systems from across the country. I can pop them in my laptop from 2009 (crappy $400 laptop from 2009) and the viewing software loads and I can navigate the images.

I can't properly interpret the images, and you're supposed to get special monitors for this type of thing, but my neurologist's monitor looks to be a generic high resolution 16:9 monitor. I may be wrong, his may have cost $$$$ for a properly certified monitor or something.

I imagine the more important thing is the EMR over network speed and security.
 

ghost recon88

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Oct 2, 2005
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As Mark R said, the images are saved as DICOM. You can use a product called Reviewer made by Sorna on a Windows PC, Osirix for OSX. Typically they are read on special monitors that are anywhere from 3-5MP using PACS software.
 

Mark R

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Oct 9, 1999
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Medical images in general are supposed to be viewed on monitors calibrated to the DICOM monitor specification.

Most generic monitors are calibrated to a gamma curve - usually around 2.2, because this gives the best preformance for TV/photo type images (and which was roughly equivalent to the performance of old TV cameras and old CRT displays). This allows good shadow and good highlight detail.

DICOM calibration is different - there isn't a gamma curve as such. Instead, it is designed so that every pixel value step is equally visible to an average human eye.

Medical monitors will come from the factory with this special calibration. Generic monitors won't, and it does make a difference, because the DICOM calibration is miles away from stock. You can recalibrate monitors, provided that they support hardware calibration, and you have suitable software (a generic calibrator like a spyder won't support DICOM - you need a specific DICOM calibration software package). I've been setting up hardware for teleradiology, and use generic 10-bit hardware calibrateable 1440p monitors and DICOM calibration software. The calibration/QA software costs almost as much as the monitors, but the combo is a tiny fraction of the cost of buying a "medical" monitor and meets all the relevant regulatory approvals.
 

MutantGith

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Aug 3, 2010
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For a bit of contrast, I just flipped over and looked at some CT data I ran for a client in the semi-conductor industry, and the specifications there are somewhat different.

The raw X-ray images are 2048x2048 Tiff files, no compression, 65K gray scale. The system takes a variable number of images, depending on resolution desired. In this case, there is one image taken each tenth of a degree. The software, VGStudio I believe, can then render that down into a ~3 Gig .vol file for processing and imaging. That process grinds a four socket, sixteen core machine with 32Gigs of RAM and an SSD array to a pathetic crawl.

But then again, the final rendered voxel dimension is under 8 microns.

Completely different application, but it highlights how widely varying the answer to the question is, depending on what you need to get out of it.

Oh, and I just remembered. Often, CT type modeling and rendering can be used to look at different structures, without using X-ray data as the source. Someone I did some work with was doing a project where they were documenting the folding and molecular geometry in the root proteins of micro-tubules in individual cells to determine what makes the little guys work like actuators. In that case, the CT 'slices' were generated by painstakingly taken short exposure TEM images, where individual tubules were imaged under fixed conditions, often under cryogenic conditions. That took an even longer time, because a number of individual samples were examined and then averaged, so there was a whole host of pre-processing, corrections, beam artifacts, etc... that needed to be taken into account.
 
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Sep 29, 2004
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Wow, lots of good info here.

Thanks a lot!

What do you all do for a living? Mark R, what's your story that you know so much including the software side of things?
 

ghost recon88

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Oct 2, 2005
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I'm a PACS Administrator for an out patient facility. Just recently did a monitor refresh so everything Mark R said is fresh in my mind
 
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