My Brain in 3D: Rendered Videos and Images of My fMRI Scan Data

My brain (c 2007).
My brain (c 2007).

Back in 2007, I made a deal with a friend to participate in his fMRI brain scan study at the University of Liverpool in exchange for a copy of the DICOM data from my scan. He agreed to the trade.

Since then, I occasionally pull my scan data off the shelf and dust off the cobwebs and disk errors, and import it into the DICOM Viewer, OsiriX (e.g., as I did in 2009). With the latest versions, I have had a lot of trouble importing the files as they were given to me into OsiriX. Luckily, I saved the installers for earlier versions including the venerable version 3.5.1, which still runs fine on MacOS X Mavericks and Yosemite.

Using OsiriX’s many features, I created these four videos and an album of images of my 2007 brain. I wonder how it has changed since that time–completing my MA, then PhD, taking a postdoc at Georgia Tech, and now, working at City Tech. Also, I think about the technologies of representation that make it possible for me to see my brain without injury or invasion–OsiriX and unseen software libraries for working with, manipulating, and displaying DICOM data, MacOS X and its technology APIs, my MacBook Pro retina, disk and flash drives, email (how I originally received the scan data), the fMRI machine that I sat in for 30 minutes to an hour, the physical laws behind each technology and the biology of myself, etc. What do you think about when you see my brain represented below?

Final Videos

Draft Video (I had not yet removed all the tissues and bone around the brain)

Rendered Images

On Watching Jurassic Park in 3D

Last night, Yufang and I went to see the new 3D version of Steven Spielberg’s classic Jurassic Park at the Regal Hollywood 24 in Atlanta.

When Jurassic Park was originally released in 1993, I saw it three times on the Saturday of its opening weekend. I was in high school, and I followed science and cinema with a singular devotion. The images of the dinosaurs as living creatures amazed me. The possibilities of science to make something like Jurassic Park a reality captivated my imagination as much as the reality of the computer and special effects technologies that breathed life into these lifeless images on the screen.

I do not believe that I have seen Jurassic Park since that important opening weekend back in 1993. Of course, I have thought about the images and techniques that made those images possible, but I didn’t return to Jurassic Park as a film experience until last night.

Yufang had never seen Jurassic Park in the movie theater, but she had seen the film several times on VHS or DVD. Certainly a smaller screen experience than what I had had, but nevertheless, it was a science fiction film that she enjoyed and wanted to experience again on the big screen. Thus, we decided to find out how the film had been transformed by 3D post-production.

As soon as the sounds and the opening titles began, I knew that we were in for an exceedingly fun experience. However, I quickly found the 3D effects more distracting than immersive. Perhaps my respect for and expectation of Spielberg’s framing choices and other filmmaking techniques created a gap between my expectation and the unequivocal thereness of 3D. While I thought that the 3D effects were interesting and occasionally exciting, I do not believe that they add anything of substance to an already important and engaging film like Jurassic Park.

Yufang and I enjoyed seeing the film together, but I was haunted by the artificiality of the 3D effects. I think that the 3D re-processing of the film created with artificial dinosaurs makes the unreality of the dinosaurs that much more present. However, I do not mean that the 3D effects make the dinosaurs seem fake. In fact, there are several scenes–particularly involving T-Rex after Dennis Nedry (Wayne Knight) shuts down the security fences–that make the dinosaurs seem more real. What I mean is that the 3D’s cardboard-cutout-ness of layered scenes (foreground, midground (action usually), and background) makes the film feel more artificial than the original 2D film. The trick that our brains play on us as we see a 2D film is far more immersive to me than most 3D films–especially the ones that have 3D added as an afterthought and money making venture. Of course, Avatar is a different story altogether that I spoke about at the 2010 Science Fiction Research Association Conference [some details available here].

Films like Jurassic Park should, I believe, remain in the precious state of 2D where our brains can give us the trick of immersion that 3D post-processing cannot provide. Nevertheless, Jurassic Park in 3D is a fun movie and I am glad for having gone on its updated tour with Yufang.

Complain If Your Digitally Projected 2D Movie is Dark

According to Ty Burr of the Boston Globe (and commented here and here), the big movie theater chains are sticking it to consumers by not enforcing the removal of a polarizing lens from digital projectors made by Sony. These lenses are what enable 3D projection technology–two lens, each projecting one polarized image in quick succession combined with the polarized lenses worn during 3D movies gives viewers the 3D effect. When 2D films are shown on the same 3D projectors and the polarizing lenses are not removed, you see a significantly dimmed image on the screen, because you are seeing only one polarity of light escaping the filter. This effectively dims the image so that even bright scenes appear dark. This problem is due to two factors: 1) Sony DRM will shut down a movie projector if certain passwords are not entered correctly when the polarizing lens is removed, and 2) no theater chain has an official policy to remove the lens when switching between showing a 3D film and a 2D film. Apparently, the fear of offending the Sony DRM-gods, time to remove the lens, and lost sales has prompted this customer-be-damned attitude by the theater chain executives. DRM sucks, but it is the job of the movie theater chain management to give customers the movie going experience that they are paying for. Last I checked, we shouldn’t pay full price for only half an image. Check for the tell-tale sign of two projectors during 2D films and the “D” for digital indicator next to 2D movie listings. If you go into a film that suffers excessive dimness, demand a refund. Read the full report here: Misuse of 3-D digital lens leaves 2-D movies in the dark – The Boston Globe.

Wall-E, Terrific Science Fiction

Yufang and I just got back home from seeing Pixar’s latest animated film, Wall-E, at the single screen Highland Theatre in Akron, Ohio.  It’s everything but a “silly cartoon.”  I have to tell you–Wall-E is TERRIFIC Science Fiction, and GREAT filmmaking!

I’ve seen every film by Pixar except for the Toy Story series, and I’ve enjoyed all that I’ve seen thus far.  However, Wall-E surpasses all of their previous work through a well-thought out story, amazing cinematography, good examples of real-world physics, and the interweaving of American consumer culture with capitalistic-paternalism and eco-disaster.  The most striking element of the film goes back to Leo Marx’s work, The Machine in the Garden, but I believe Wall-E is emblematic of how Marx is wrong.  Marx’s thesis is that American literature imagines an idyllic garden which has been lost and is reattainable through the embrace of technology, but the lost Edenic pastoral is gone forever, and technological progress pushes us further away from it.  The characters of Wall-E and his girlfriend, Eve, show humanity the way toward regaining what we’ve lost through two key scenes (one in the film, and the other during the end credits).  The earlier scene has Eve take Wall-E’s plant offering into what is best described as a womb.  There, the plant is safe until returned to the corporate robot controlled Axiom starship (accepted/unquestioned truth, wow, what a perfect name!).  Wall-E and Eve keep the plant safe, and reawaken obese humanity’s connection with (mother) Earth.  Then, during the end credits, there are developing scenes in a variety of stylzied animations covering cave paintings to Egyptian heiroglyphics to Impressionism.  In these scenes, the garden is recreated by the cooperation of humanity with its autonomous robotic creations.

Wall-E is a really fun movie for all ages, and I guarantee that you’ll be as enchanted as I was by this amazing Science Fiction allegory!

Watch some clips and trailers for Wall-E here.