tomographic topography by jacob ford

A three-sentence crash course in popular brain scanning
technologies: MRI stands for Magnetic Resonance
Imaging and reveals the structure of the brain. PET—
Positron Emission Tomography—shows the level of
metabolic activity, which it does by infusing the patient’s
blood with a radioactive tracer, then measuring the areas
of the brain which accumulate the most radiation. An
MRI is useful for detecting physical anomalies in the
brain, PET for determining an area which may be behaving
strangely, or become active when a patient thinks about
love.

Though the MRI does not betray it in its name, both it
and the PET are tomographic imaging technologies: they
capture one infinitesimally thin slice of the brain at a time.
Multiple slices may be stacked and then interpolated to
produce a three-dimensional view, but the result of each
scan remains one plane of data. Literally, an x–y coordinate
plane containing a grid of points, each point imbued with a
value.

Humans are remarkably bad at deriving meaning from a
grid of numbers. While most of us can quickly determine
the larger of two values when both are presented to us, we
can imagine our confusion multiplying and efficiency

until distinguishing between two very close values becomes medically necessary.1 and 0. Ruth Leavitt’s computer display in The Andromeda Strain. we are stuck reading each digit and mentally comparing values. might be an imperceptible distinction between very very very very dark grey.2. And so.1 and 0. by Brian Murphy grayscale image. This works wonderfully. in order to be meaningfully read and interpreted by humans.2. Wagner Jr. The result is 18-FDG Normal Brain. [In lieu of imagining. and all interstitial values mapped to corresponding shades of gray (Picturing Personhood 91). in Picturing Personhood 90). The difference between 0. posits that the resultant data from a MRI or PET scan “can only be abstracted and displayed in a meaningful way in the form of images” (qtd. then. where the brighter points represented denser [MRI] or more active [PET] areas of the brain. Still from The Andromeda Strain. reproduced in the left margin. For the sake of this example. 1971 Henry N. and very very very dark grey. . plummeting if we were presented grid where each cell was populated only by a number. we will disregard units and assume that the possible values fall between zero. the lowest to black.] Because there is no implicit hierarchy in the shapes of our numerals. see Dr. mapped to pure white. say 0. the values generated by a MRI or PET scan are mapped to color values. The highest recorded value might be mapped to white. which is mapped to pure black. and one.

. So. Easily distinguishable. With training. these new color gradients allow small variations in values to map to vastly differentiated colors. or purple and green. 0. a plethora of alternative color gradients were developed.2 might display as blue and red.1 and 0. Perhaps ranging through the rainbow or alternating between bands of contrasting colors. But color introduces a new set of rabbit holes. Now. by Brian Murphy white. a neuroscientist well accustomed to a specific gradient might be able to quickly discern fine details in the scan data simply not detectable in black-to- 18-FDG Normal Brain.

and possibly despairing (Society of courtesy JNMT Nuclear Medicine). but is in fact the exact same PET scan mapped to 41 distinct color gradients. to draw neuroscientists’s attention to the issue at hand: that the visual disparity of the images is beautiful. at Buffalo (Picturing Personhood 94). The above is not a grid of 41 distinct brain scans [the upper left and lower right are identical]. According to Murphy: The effects created by various color scales may be visually dramatic. And gone is the inherent hierarchy of black-to-white color gradient. It would seem that the rainbow would carry an equally evident hierarchy of values. The images were compiled in 1996 by Brian Murphy. With so much image analysis occurring on the computer where dialing up any color scale you like is relatively easy. it is possible to make almost any feature stand out with the right “tweaking” (affectionately referred to as “dialing a defect”). at that time the director of computing and the PET clinical physicist at the Deparment of Nuclear Medicine at the State University of New York. but may also cause one to see distinct boundaries where there are none. a simple technicolor . The grid appeared on the front cover of the Journal of Nuclear Medicine Technology in December that same year.

or apparent in the first place. by Brian Murphy a disproportionate amount of contrast into one small area to make a correlation more apparent. something simply not true in all gradients. publications may— knowingly or unknowingly—take advantage of an untrained viewer’s naivety. leading to confusion when red appears in the middle or even at the bottom of a gradient. We might consider red to be urgent. and instead demands constant cognition.0 and 0. Like our earlier grid of digits. by Brian Murphy numbers they represent” (Tufte 92). values between 0. crafting a gradient which packs 18-FDG Normal Brain. We might presume different shades of the same color indicate values close to each other.2 were all colored similar shades of purple. On a more nefarious level. transposition of the black-to-white gradient. but “despite our experiences with the spectrum in science textbooks and rainbows. or hot. the mind’s eye does not readily give an order to ROYGBIV” (Tufte 92). while . Another problem: we’ve imbued certain colors with cultural significance. “now and then reduc[ing] perplexed viewers to mumbling color names and the 18-FDG Normal Brain. See for instance a 2004 article in Science which further skewed some images from a National Institute of Mental Health study to make it appear as if virtually all gray matter vanished by age 16. In reality. the rainbow which seemed so thoroughly above arbitrariness quickly loses its power of immediate recognition when it is mapped to data.

Furthermore. each medical school has adopted a favorite gradient. into a land where “multiple layers of statistical and mathematical processing” are required to even make that data human-readable (Delehanty iii). those between 0. We’ve moved well beyond the realm of data- producing machines. but they become dependent on abstractions. Beckman 597. further distancing themselves from the data itself. When we are not analyzing the data itself but an abstraction of it. They may be immune to the emotional significance of colors and they may be able to ward off attacks by poorly constructed gradients. “The ability of the user of the data to make certain types of . and students emerge from each school experts in reading PET data colored exclusively in their chart reproduced from Beckman 597 school’s preferred gradient (Picturing Personhood 94). orange. or even blue (How (Not) to Do Things with Brain Images 302. green.3 and 0. it’s discomforting that something so precarious as an individual neuroscientist’s color perception or the color settings of a screen could alter the interpretation of a brain scan. yellow. But even well-trained scientists have their own set of issues.5—ta span of the exact same size —could be bright red. a miscalibrated pixel or poorly configured printer might be held responsible for misrepresenting data. Gogtay 8178). By now. because so much now hinges on images.

I propose that we halt the use of color altogether. and valleys define the opposite. like a three- dimensional line graph. scientists can stop training to become experts at arbitrary color scales. .discriminations is affected both by the data production process (constraints imposed by features of the object- representation relationship) and by the data display format” (Delehanty 162). As said in this paper’s second paragraph. and I believe it is time to create something less divisive and more decisive. each point imbued with value. the result of a brain scan is “literally. Either by manipulating this model on computer interface or using it to produce a tangible object with a 3D printer. an x–y coordinate plane containing a grid of points. I want to change the data display format. And so. and instead tap into something all of us have been practicing since birth: spatial reasoning. We are arguing more over how to look at the brain than over what we actually see. it is simply too arbitrary and inherently meaningless.” All we have to do is use that value to determine that point’s height. and we have define a mesh of brain activity. I propose we map brain scan data to three-dimensional space. Peaks define areas with higher brain activity than their surroundings.

In fact. I had only to extrude from it a flat-bottomed surface so that the model could be printed. land elevation values for a predefined swatch of earth are mapped to a gradient: the highest possible value becomes white. called a GeoTIFF. and the result is an image example GeoTIFF file. One of the simplest and most popular methods for storing terrain data is no more than a glorified image file. The background scatter radiation which was confusingly bright in some gradient images now becomes distinct but . It is a process virtually identical to our first black-to-white gradient image. These analogies to topographic features are not a coincidence. but which requires only a quick script to be converted into a 3D model. and all others to corresponding shades of grey (Ritter). I took two of Murphy’s PET scan images which utilize a black-to-white gradient—one scan which used 18-Flurodeoxyglucose as a tracer and one which used water but both of which model a healthy normal brain—and imported them into 18-FDG Normal Brain. from WolframAlpha documentation highly readable to humans. by Brian Murphy. the lowest black. To make one. Thinking it was mapping some curious butte. after being processed and extruded in AccuTrans3D AccuTrans3D. the models for this very project were generated using software intended for converting GeoTIFF files into printable 3D models: AccuTrans3D. the software had within milliseconds generated a mesh from the scan images’s color values.

which is obvious in the center. We could even imagine a blind neuroscientist able to use her refined sense of touch to investigate the brain more intimately than any sighted neuroscientist can today. the result of AccuTrans3D analyzing the gradient included on the right side of Murphy’s scan images. look straight down or prod with a measuring stick to find the lowest valley. To find the least active. immediately after being become useful tools in measuring and comparing brain read as a GeoTIFF in AccuTrans3D activity. a PET scan of a brain with a tumor [softtware model and image at left] becomes instantly comprehensible. simply hold the model at eye level and search for the tallest peak. While I imagine the two models of healthy brains produced for this project as training tools. But when questions arise or Top: original 18-FDG Tumor Brain scan. is a wonderful built-in data integrity check. To find the most active area in the scan. and a useful orientation tool as well. the age-old caliper or level could Bottom: same image. To analyze a 3D- printed brain scan is to utilize spatial skills we’ve already refined over a lifetime. instead of tedious investigations into the color of particular areas of an image. The perfect ramp along the right. not distracting from the brain proper. even to the untrained eye.
 . by Brian Murphy [basis for Bottom] precision is necessary.

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