A 3-D View of the Brain

Jamie found a nifty story about Researchers at Thomas Jefferson University Hospital coming up with new 3D Brain Imaging Software. The interesting bit is that it merges data from MRIs as well as various other types of brain scans to create a single visualization for your noodle.

Check out the 'MultiMedia'

[Silver Sloth]

As well as TFA there's a 'Multimedia' link which give much more info - as well as having some pretty pictures.

Re:

[morgan_greywolf]

OMG, tt's yarn [technologyreview.com]! The brain is full of yarn!

Oblig..

[jd]

Imagine a beowulf cluster of brain-imaging systems...

That will be $213,134.56, please.

[xxxJonBoyxxx]

There's your referral. That will be $213,134.56, please.

Matching images.

[iknownuttin]

The interesting bit is that it merges data from MRIs as well as various other types of brain scans to create a single visualization for your noodle.

FTFA:...including conventional magnetic resonance imaging (MRI), functional MRI (fMRI), and diffusion-tensor imaging (DTI).

They're all forms of MRI. Unless there's a MRI machine that can do it all, it would seem to me that you would have to have the patient go from one machine to another. I'm curious how they match up the structures exactly from one scan to an

Re:Matching images.

[tOaOMiB]

All MRI machines can do it all; they are just different programs you feed the machines to get different images. Unfortunately, the images at the end still have to be lined up. This is typically done by allowing the brains to rotate in 3 dimensions until the registration maximizes some function; for example, the mutual information between the two images. See the package fsl (http://www.fmrib.ox.ac.uk/fsl/) for some great fMRI analysis tools, including FLIRT for aligning brains (of multiple patients, or one patient's fMRI scan to MRI scan).

Re:

[glueball]

they're relatively easy to match up!


Not always true. A GRE, SE, or FLAIR image sequence for anatomy will not line up well with the EPI sequence of fMRI due to B field non-linearities and shift even if the patient doesn't move. The nice thing, though, is that unless there is surgery and deformation due to swelling, tissue void, or skull shifting, the skull shape stays constant and one can use it as a rigid body for starting the registration.

There are some software programs to attempt it but it still comes

Re:Matching images.

[MillionthMonkey]

Fortunately, most brains (unlike arms and legs) aren't in the habit of moving around a lot during an MRI scan, so they're relatively easy to match up!

You've obviously never spent an hour inside one of those machines. I used to do research in an fMRI lab and even something like post nasal drip eventually makes you swallow just to keep breathing and the slight movement pushes your head into a new pixel lattice so when you subtract the images you just see gray everywhere.

Re:

[glueball]

Or are you suggesting that your brain actually moves around inside your skull when you swallow..?

The brain really moves the B field during swallowing, resulting the the brain apparently moving.

Re:

[MillionthMonkey]

The field isn't jarred too much because the brain has low magnetic permeability and it doesn't dictate the field topology. But your skull moves enough for subpixel displacements to skew the later analysis. I used to hate these experiments. They all had to be done at 3 AM because the machine was constantly in use by paying customers. We were measuring pain, too, which really really sucked for a bunch of reasons:

- Nothing shows up on an fMRI (it seems a few neurons fire somewhere and you're in excruciating pa

Re:

[buswolley]

My thought exactly... I swore I was showing a subject their brain in 3d just the other day after their run through our fMRI memory study.

The machine takes many 2-d image slices, and a program aligns them into a 3-d model.

We all know what a man's brain really looks like-

[tomhudson]

http://www.suddenlysenior.com/Images/malebrainwome n.gif [suddenlysenior.com]

Re:We all know what a man's brain really looks lik

[struppi]

Yea, but TFA said 3D image of The Brain [flickr.com].

The ultimate geek

[GregPK]

Would order pictures of his brain and keep one on his desk in a frame.

I'm such a dork, because I kinda want one too. :-D

Re:

[normuser]

No, no, I'm afraid, GrekPK, that it's only you.

No, he`s not the only one.
I would love to have a picture of my brain.

Re:

[talljuan]

For $2-3000, you can. Just go to any MRI facility and make an appointment.

The alternative is to get to have it prescribed by a Neurologist, and then your medical insurance should pay for it. At least, that worked for me.

In my case, I am actually able to say the following:
    <ahnold>It's not a too-mah. Wait. It IS a too-mah!<\ahnold>

(yes, I did in fact have a brain tumour)

Re:

[xaxa]

No, the ultimate geek makes a 5 metre by 8 metre (I'm guessing) colourful brain scan and sticks it to the wall of a university.

The identity of the brain scan, in the main College entrance - a closely guarded secret until now - was revealed before The Queen departed. "The Queen asked whose brain it was and Jo Hajnal said 'it's mine,'" said Danish artist, Per Arnoldi, who worked with the professor, an imaging scientist at the Hammersmith campus, to create the visualisation.

http://www.imperial.ac.uk/p5374 [imperial.ac.uk]

Re:

[thatskinnyguy]

I think I lost all faith in /. peer moderation. I drop a Star Trek reference and get modded-down while some other guy talks about titties and beer and gets praised. *shakes head* [/whining]

Re:

[$RANDOMLUSER]

While I'll grant that Dr. McCoy is important to the /. community, I'll submit that titties and beer are sacred.

Not likely

[$RANDOMLUSER]

If it really was a 3D representation of my brain, all you'd see would be tits and code (and maybe some beer).

for the lazy

[bumby]

http://www.technologyreview.com/player/07/08/06Sau ser/1.aspx [technologyreview.com]

nothing new

[j00r0m4nc3r]

Computer-assisted stereotactic neurosurgery has been around for a long time. The software takes MRI slices and uses a marching-cubes-type algorithm to convert from texels to voxels. I don't see how this software is anything new really, other than maybe using some other kind of input image.

Re:

[chrplr]

The program displays fiber tracks computed from the diffusion tensor images. This involves more than just fusioning images from different modalities (fiber tracking is far from obvious). Also, some images are 3D surfaces reconstructed from 2D slices. This being said, it has been possible to make and manipulate this kind of images for a while with the (freely available) program "anatomist/brainvisa" (cf. www.brainvisa.info).

Nothing new here...

[perrin]

I work within the field of medical imaging, and this is nothing new. People have been doing image fusion with images from different image modalities for over a decade. There are lots of products like this one, some even open source and with more impressive screenshots. Why is this particular product, which is not even named or referenced, featured? If you want to see impressive open source work within the medical world, check out ITK and VTK (http://www.vtk.org/ and http://www.itk.org/ [itk.org]). Now that is really cutting edge work done with free software.

Re:Nothing new here...

[cbelt3]

.. a decade.

How about over THREE Decades. As a high school student (in the 70's), I worked on software to merge CAT scans and thermal scans of the brain during an NSF summer program at Mizzou. Fortran IV, big honkin IBM 360 mainframe, etc. The first run with a full data load took the entire University mainframe down (hey, I was only 15 and didn't understand JCL, shoot me). We were trying to auto-diagnose tumors.

The basic engineering has been refined, but the science is still the same.

Re:

[RockoTDF]

I doubt your mainframe in the 70s could render 3D imagery...so I don't think this is 3 decades old.

Re:

[cbelt3]

Yes it could. It's not the rendering math, or the 3d basic algorithms that have experienced advances (although they have). It's the resolution of the sensors. Our brain scan was a cube approx 1024x1024x1024. That was a boatload of data for the 70's. The ones discussed are ginormous data sets.

Re:

[RockoTDF]

But could you view and rotate the brain, or was this a CLI type thing? I mean 1024x1024x1024 is probably enough for detecting tumors or brain damage, but neuroscience requires more which is why this article isn't as irrelevant as some are saying.

Re:

[cbelt3]

Oh, you were looking for a display, and maybe a mouse and overlapping WIndows ? Sorry, hadn't been invented yet. We did build a color map display and rotate it, though. This was the Biomedical Image Analysis Lab. Very cool stuff for 1975. Imaging and display ran on a PDP-11...mmm. back in the day. had to boot that sucker by loading in the punch tape boot code sequence in octal, then load paper tape, THEN we could actually load the programs from Mag tape. you guys and your newfangled hard drives don't know h

Re:

[eozh]

Actually, clinical MR images rarely go beyond 512x512x200.

Re:

[RockoTDF]

Yeah but in any science or medical field there is always a difference between the clinical usage of something and what scientists need to do the base research.

Re:

[Anonymous Coward]

I was also disappointed to not have the package/link to the software mentioned. I'm pretty sure that this article, posted Aug 3,2007, can provide a bit more detail - there they use MediCAD:

http://www.sciencedaily.com/releases/2007/07/07073 0173404.htm [sciencedaily.com]
http://www.cs.sunysb.edu/~vislab/papers/Xin_ISMRM. pdf [sunysb.edu] - paper from Thomas Jefferson University and Stony Brook University

Other posters here note the concept is not unique; but perhaps using it for surgical procedures regularly, rather than pure research, migh

Re:

[mclaincausey]

Nothing new unless you bother to RTFA.

PET/CT scanners can produce coherent datasets that can be fused by a simple overlay, and software like Mirada 7D Fusion (which we [vitalimages.com] integrate with) can fully deformably fuse all sorts of datasets from differing modalities. This is usually a 2D overlay, and it looks different than what this software is doing. They are claiming that specifically fibrous tumor growth can be visualized in new ways. So perhaps the fusing isn't novel, but the method of fusing and/or vis

Re:

[perrin]

I did RTFA. 3D image fusion is not new, either. There is a lot of exciting research in the area, though, and if they had spoken about new ways to accurately co-register different image modalities, it would have been interesting, but this was apparently all about visualization, which is not. I am also not all that much of a fan of completely merging image modalities. It can be useful to get an overview of where you are, but I am afraid you could easily lose important tissue boundaries since the algorithms us

Re:

[Bohnanza]

Who says the human brain came about by accident? Evolutionary theory certainly does not say this.

Re:

[ChromeAeonium]

You're half right. Evolutionary theory states that the best random mutations survive. Due to their superiority, the survival of organisms with beneficial mutations(and therefore, their ability to pass on their genes) is not random, however, the existence of their desirable traits is purely random.

In other words, the brain in its entirety, as a compilation of traits, would not be random, but each and every individual function would be. I believe that the point that the parent poster was trying to mak

Re:

[Bohnanza]

I do understand what the parent poster was saying, and it points out the great misconception of those who see "intelligent design" in greatly complex organisms. I believe this great complexity is a sign that we are NOT intelligently designed. Take, for instance, the human immune system, or in particular the inflammatory system. There are many different systems functioning, many at cross purposes. And the effect of inflammation is rarely beneficial to the organism. I would hope that an "intelligent" designe

Re:

[ChromeAeonium]

Huh? Inflammation raises the temperature of a specific part of the body to kill, or at least inhibit the growth of, the infecting pathogen. It's not good for the organism, but its not good for the causative agent, either.

I can't say I understand what you mean when you say that a system as complex as the immune system (what with all the differentiated cells, specific antibodies, cytokines directing cells, the compliment system, the antigen recognition and memorization of the adaptive immune response, ect.,

"noodle"

[jo42]

My "noodle" is nowhere near my brain...

Re:

[B4D BE4T]

Same here. Although I tend to get into trouble for thinking with that noodle from time to time...

House

[Elsapotk421]

great...now Dr. House will be ordering up a million of these on every episode.

Not really a new thing

[fragMasterFlash]

While it is good to see more talented people working in the medical visualization space, this is not really a new thing. Image Fusion [wikipedia.org] has been around for a while now but it has not yet become a mainstream technique.

Re:

[magbottle]

> While it is good to see more talented people working in the medical visualization space,
> this is not really a new thing. Image Fusion [wikipedia.org] has been around for a while now
> but it has not yet become a mainstream technique.

It is very mainstream for PET/CT fusion. Many manufacturers make combo PET/CT machines for just this purpose since the acquisitions are done at the same time, they align very closely and little if any rotation/translation has to be done for a good volume match.

New Dizzy Dean quote

[Bohnanza]

The doctors created a full 3-D image of my head using multiple imaging technologies and found nothing.

Getting close

[dissy]

One step closer to Mind Uploading [ibiblio.org] :D

The Mind Uploading home page is dedicated to the putative future process of copying one's mind from the natural substrate of the brain into an artificial one, manufactured by humans. This technology will radically alter society in many ways, as science fiction authors have begun to illustrate. Through this server, explore the science behind the science fiction!

-- Dissy

10 years ago

[broothal]

"That is why I am excited about something that should have been here 10 years ago."

It was. I actually wrote my master thesis about it exactly 10 years ago. But one thing is the technology. Another thing is someone to fund the development of a fully functional package. Technology is many years ahead of reality when it comes to medical imaging.

Re:

[jonscilz]

so true!!! my entire senior design project dealt with biosignal analysis in a drowsy driver simulation. we have working models just not in commercialized forms. the technology and science is way ahead of reality in biomedical engineering fields. its sad that the fda and large private companies control the rate of growth and release of these technologies!

This is your brain

[VinB]

... and this is your brain on Dual 768MB Nvidia GeForce 8800 Ultra graphics cards.

My Brain

[Coppit]

A friend of mine was doing fMRI research and was kind enough to give me the data she got from my brain. At the time AFNI was the best software for converting the data to movies. The software wasn't exactly easy to use. Since then I think the options have gotten much better. Anyway, here's my brain [coppit.org]. I especially like the axe-to-the-head [coppit.org] view.

Re:

[dogmatixpsych]

I hate to say this, but as someone who deals with MRIs of brains pretty much every day, there is something seriously wrong with your brain!


Ok, I'm just kidding. It looks perfectly normal. (I wasn't kidding about dealing with MRIs on a daily basis though). Nice images; thanks for the links.

Getting your data

[gr8_phk]

My wife recently had an MRI done (She's fine). The thing that struck me was this: On the way out to the waiting room they told her to wait a minute while they made her CD. They handed us a CD containing all the slice images (DICOM) and an auto-run (yea windows) program for viewing them. I always thought it would be cool if you could get your scan data, but here we didn't even have to ask - they just hand it out. I figured the hospital would be afraid of some perceived threat of getting sued. I also wonder i

Re:

[talljuan]

In fact, they do give you the CD if there is something obviously wrong.

After many episodes of Really Bad Headaches, I finally had a scan prescribed. I noticed that the tech and assistants seemed to look at me quite a bit differently after the scan. It turned out that I in fact had a tumour and a very large cyst which would have been immediately obvious to anyone, no medical training required. In retrospect, they were probably thinking "you shouldn't be walking around with that thing in your head!" about

not news

[jonscilz]

this is not new! we have been doing this in the CILab for years at rutgers http://biomedical.rutgers.edu/faculty.php?id=23 [rutgers.edu]

Old News

[conspirator57]

SGI Volumizer did this like 10 years ago...

http://www.sgi.com/products/software/volumizer/ [sgi.com]

The Original Project

[big dumb dog]

I think I heard that this software project originated in Redmond, but it failed in the QA process when they were unable to find a brain to test it on. (...it's a joke)

FYI,one way to compute 3d brain models from MRIs..

[syn1kk]

is done through the application of 'level sets' its pretty fun stuff to study. There are some cool videos of level set stuff like this one: http://graphics.stanford.edu/~fedkiw/animations/wa ter_oil.avi [stanford.edu] . And the application of level sets is very broad. I've only dabbled in Level Sets but I am very tempted to do a Master's thesis on it =P.