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Tuesday, January 15th, 2008

Astronomy Therapy

A couple of nights ago I had an awful lot on my mind, and despite thinking that I really needed to go to bed and get some sleep, I went outside and looked up.

It was a cold, clear night, and viewing by the naked eye was probably as best as it could get (unless you happen to be driving across the middle of nowhere in New Mexico.) Even so, I grabbed a pair of low power binoculars and was rewarded with huge new perspectives.

I’ve been trying hard over the last year to finally learn something about the stars at night. I’ve always been interested in space, but never bothered to learn any astronomy. When I first started playing with Linux I encountered KStars and loved it, then I found Stellarium, which is even better, and I could load a copy on my Windows machine. I started in the summer and learned the basics – the Summer Triangle (Vega, Deneb, Altair), Rasalhague, Polaris, Cassiopeia, The Big Dipper, Arcturus, and Spica. Jupiter was in Scorpio, near Antares, and as the season progressed (or if I stayed up really late), Andromeda crept up. I knew there was a galaxy there but couldn’t find it. When I went to Diego Garcia I got up at 4 o’clock in the morning to go out for a sighting of the Southern Cross. Unfortunately, there was no way I could see Alpha Centauri again that time of year.

But I longed to see Orion again, and to really try to learn about the northern winter stars. So this night was the time to really delve, and I was rewarded.

I saw Orion, with Betelgeuse, Bellatrix, Rigel and Saiph. And I saw the Winter Hexagon, with Rigel, Sirius, Procyon (which I learned to pronounce), Castor and Pollux, Capella and Aldebaran. I watched Regulus in Leo come up, and saw Saturn. Mars was just underneath Alnath. And I pulled those laughable little binoculars out. I couldn’t see Saturn’s rings, but I saw the little fuzzes of the Great Nebulae in Orion and Andromeda. I located my own Zodiac sign – Cancer – and also discovered the cluster Praesepe without knowing to look for it. I finally found out why the Pleiades were so cool (although I don’t know why they’re called the Seven Sisters – I count six, and several possible contenders for the seventh.)

With the help of the binoculars, and my laptop with Stellarium (and Wikipedia to answer questions, and a couple of tequilas to keep me warm) I was able to actually see constellations. I saw Leo and Canis Major. I saw Hydra’s head (I used it to find Cancer), and Gemini, Auriga, Taurus and Perseus. I don’t know why Andromeda is a woman’s shape, but I saw where the stars were. I even lucked out and saw a meteor go across half the sky, and two satellites plod away. I recognized the motion from seeing Skylab before it fell in 1979, just before I left for America. I want to know why Cancer is listed as “small and dim” on Wikipedia when Pisces is even dimmer – what is that, “large and even dimmer”? I want to know why I’m considered to be a Cancer when the Sun was actually in Gemini when I was born. No, wait. I read about the difference between tropical and sidereal zodiacs – it just makes my head hurt, and astrology is all a bunch of BS anyway.

I went to bed when I realized that I had watched Procyon rise and now Arcturus had been up for a while – Spica was about to be visible again. Amazingly, considering the amount of warming I had turned out to have required, the next night I still was able to reel off a bunch of these names that I had learned.

If you want to lose yourself for a while, go outside at night with binoculars and Stellarium and Wikipedia. Take a friend if you want – maybe José or Jim or Johnny.

Posted by Greg as General Science, Posts About Me at 22:02 PST

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Sunday, March 25th, 2007

Funny APoD

I had to laugh at today’s Astronomy Picture of the Day, NASA’s daily picture and “brief explanation written by a professional astronomer”, usually chock full of links. The picture was the famous 1972 pic of the Earth, as taken from Apollo 17. The write-up concludes:

… Earth supports a large variety of life forms, including potentially intelligent species such as dolphins and humans. Please enjoy your stay on Planet Earth.

“Potentially intelligent?” I’ve been trying to think of some snarky comment about that, but the more I thought about it, the more I tend to agree.

Posted by Greg as General Science, Society at 00:49 PST

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Thursday, December 28th, 2006

High Desert Snow

I’ve been doing a lot of traveling lately, but today, instead of flying, I was driving. I was passing through the Galiuro Mountains east of Tucson, heading for New Mexico, and it was snowing lightly.

Snow in the high desert is just the icing on the cake of the beauty of this land. I’m sure there are places in the American Southwest that are even more spectacular, but it sure was nice being distracted from the things that are going on in my life by a few incredibly picturesque scenes.

Geography has a major consideration in my work of late – I’ve been tracking cathodic protection readings by GPS readings. Although I first started trying to get geographical coordinates on CP facilities (and by extension, the structures that they’re on) back in 1995, the available technology has improved substantially over the years to the point that very accurate information is easily obtained. The trouble is, the tools to manipulate this data have not been so forthcoming. I’ve been keeping my eye on GIS systems for a while now, but the software has been prohibitively expensive for me to use with what I’ve been doing. But that’s changing – GIS has become a foundation for all kinds of civil engineering work and other fields, and now corrosion control data analysis is being dragged into it. Clients are just now starting to demand their data in a GIS-importable format, and I’ve got a whole new skill set to acquire.

But this skill set combines a lot of things that I’ve already been interested in – map reading, computer graphics, and databases. I’ve been boning up lately on the fundamentals, particularly on the basics of geodesy (projections, datums and coordinate systems). I’ve been trying to get a high end open source GIS system installed on my computer, but the Windows version just doesn’t work, and the Linux version seems to be having a lot of problems with dependencies, which is also helping me get more familiar the nuts and bolts of Linux, because I’ve been trying to configure and compile source packages instead of installing rpms.

But if that wasn’t enough to keep me busy, while researching the geography of the region, I couldn’t help but get drawn into the history. I ended up with a fascination in Sibley’s 1862 New Mexico Campaign, which turned out to be the historical setting for one of my favorite movies – Sergio Leone’s The Good, the Bad and the Ugly.

Yeah. Distractions. May as well put them to good use.

Posted by Greg as Corrosion Control, General Science, OS, Posts About Me at 21:59 PST

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Wednesday, June 7th, 2006

Headed for Surgery

Apparently, my surgeon was wrong about the lymphedema. (I’ve stopped trying to finish the MRI story for now – I hope to get back to it.) The MRI results came back, and I definitely have a “lesion”. Instead of continuing to try and figure out what it is, we’ll wait for the lab results after some technician cuts up the whole thing and puts it under the microscope, or whatever it is that they do, because I’m just going to get the whole thing cut out. Surgery is scheduled for next week – Thursday, 15 June, at 1400 PDT.

We have a fairly high degree of confidence that whatever it is, it’s not malignant, thanks to the PET scan, so I’m only running a small risk that I’ll have to go back under the knife to remove more surrounding tissue. I’ll be getting general anesthesia on an outpatient basis, and hope to be back to work quickly, although I’ve requested the following day (Friday) off as well. The Incident of the Mysterious Lump is going to come to an end.

Posted by Greg as General Science, Melanoma, Posts About Me at 18:15 PST

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Thursday, June 1st, 2006

My First MRI – continued

*** This is Part 2. Part 1 is here ***

Phew. Had to take a break. I’m fascinated by all the technology involved with this, so it’s even harder than normal to contain my curiosity about every little facet, and I spend more time searching than writing. I did, however, manage to identify the raised platform with breast holes and the framework the techs were trying to strap on to me – they were RF coils. I was trying to elaborate, but the Wikipedia MRI page is like a huge black hole that keeps trying to suck me in, and I want to get back to the story. (There’s also a pretty good layman’s article at How Stuff Works, and an every-little-detail package at The Basics of MRI.)

So I was wedged into this tube, trying to stay relaxed, and the noises started.

An MRI doesn’t sound anything like somebody beating on a can. It was loud, but with the earplugs, not painfully so. What startled me was the nature of the sound – it clearly wasn’t mechanical. It had lots of buzzing and resonating thumping, and it wasn’t constant or even regular. There were frequent pauses before the next sequence of sounds started up, and each sequence had a different pattern, which caught me off guard each time. You can go off site to hear sample sounds – I haven’t found a good embedded player for WordPress yet. The noise is caused by the harmonics induced by the rapidly switching magnetic fields.

Although the magnetic fields inside an MRI are incredibly strong – thousands of times the strength of the Earth’s magnetic field – we supposedly aren’t capable of sensing them. But at times I felt something. Most often it was like a very faint sensation of having all the hairs on your body stand up at once – then start wiggling really fast. But I also felt weird, indescribable feelings of pulling and twitching throughout my body, and flashes of heat. It could have been entirely psychosomatic, I guess. Apparently, the only established effects of exposure to strong magnetic fields are vertigo and nausea. Prior to my scan, I had to go over a list of implants and other foreign materials that would be adversely affected by the strong fields, or that could have an adverse affect on me when they reacted by moving closer to the magnets. I didn’t see anything to worry about.


Posted by Greg as General Science, Melanoma, Posts About Me at 00:08 PST

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Sunday, May 28th, 2006

My First MRI

Early yesterday evening I went over to Sharp Memorial Outpatient Pavilion for a scheduled MRI (my first one ever) to confirm my oncological surgeon’s recent diagnosis of the lump in my chest as a lymphedema. By which, I’m assuming he means “mild case of…”, because after recently learning the difference between lymphedema and the more general edema (the latter was what I thought my original surgeon had warned me about after my surgery to remove lymph nodes), I did some research and found some really bad horror stories – with pictures. So it’s hard to put the words “lymphedema” and “good” in the same sentence; but if true, the lessor relief is that I will not need surgery. I was very concerned that the lump is either a metastasis of my original melanoma or a case of male breast cancer, since the women in my family seem to be pretty good at getting it. So lymphedema, especially since it’s already getting smaller, is acceptable, I guess.

Earlier this week I was trying to encourage someone to not be afraid of taking a PET scan, which all the while seemed a little silly, because pretty much the hardest thing I found in the three I’ve taken was staying awake – I have a tendency to roll onto my side when I fall asleep. And snore. Really loud. I mean, REALLY, REALLY loud. But if Andrea had ever taken an MRI before her first PET scan, it would all make sense.

I had heard the your-body-in-a-tin-can-and-somebody-banging-on-the-outside-with-a-big-stick simile so many times, it was all I was expecting, and it didn’t sound too bad. I don’t consider myself to be claustrophobic, and we have a two-year-old at home, so someone always seems to be a) banging on something with a stick, or b) yelling about it. I figured I would still have to worry about falling asleep.

Looking back now, it wasn’t really all that bad an experience; but it was unpleasant, and unpleasant in ways that I wasn’t prepared for. When I showed up, the tech, as usual, got this worried look and started asking questions about my height and weight. I’m used to that, for these imaging techs always seem to be going by the conservative guidelines published by their equipment’s manufacturers, who don’t want the liability, and who either don’t know or don’t care how much more an enthusiastic and enterprising person can stuff into an orifice. But in my particular case, “stuffing” is an apt description of how we got my 195 cm (6′ 5″), 122 kg (270 lb.) frame into the desired area.

First, I had to get an IV set up. When I asked them to use the tourniquet as briefly as possible because of my lymph node removal, they decided that they needed to consult with somebody for instructions. While they were on the phone, I tried using my thumb to press deep between my biceps and triceps muscles to try to squeeze off the brachial artery, and flexed my arm muscles to try to get my veins to pop out a bit. I wanted to make the veins in the cleft of my elbow more prominent so that they wouldn’t have to use the tourniquet. Lymph has a much smaller, distributed circulatory system, and I figured that if I could directly manipulate my blood vessels, I might have found a way to get blood drawn (I seem to be getting blood drawn on a regular basis nowadays) while reducing the risk of lymphedema. While I was thinking this out, I realized that I was attempting to shut off the blood supply while looking for an effect that was caused by reducing the blood return. See? I’m not afraid to expose my ignorance to my readers! Somehow, probably just through the muscle clenching, I got a vein to stick out and I went ahead and got poked sans tourniquet. While I was being hooked up, I inquired as to what was being pumped into me, and was told that is was a contrast agent containing gadolinium, which is used because it is one of the few elements other than iron that is magnetic.

Next, I had to get into position on the bed of the MRI scanner. Here’s a small picture of the machine – I have so far tracked it down to one made by Phillips, of the Achieva line – when I learn more, I’ll post it.)
Phillips Achieva MRI scanner
The bed was fitted with a raised platform with apertures for breasts – up to rather large breasts, as I can see from the sample images at the Phillips site – but that didn’t help me and probably took away room inside the scanner that I later would have preferred to have had. I lay on my stomach with my arms extended ahead of me, and my head propped up on pillows and turned to one side, with my face resting against my right arm. It seemed pretty comfy, and there wasn’t any part of me to hang up the IV tube, and they proceed to strap me in, securing some sort of framework on my back. I tried the headphones – they were offering music – but it was either have my face stuffed into a pillow or the earpiece jammed into the side of my head, so I opted for earplugs instead. Then we tried sliding the bed into the bowels of the machine. Right away, it was clear that it wasn’t going to work. There was barely enough room for my shoulders, let alone the framework on my back, so they pulled me back out, removed the framework and slid it under me, and tried again.

At first I thought there was plenty of room, but the hole apparently had two stages, and as I was carried further inwards, my normal chest size of about 142 cm (56 inches) felt like it was being reduced a good couple of inches. My guttural and vocal reaction (!) caused the movement to halt, and there was more consternation. The tech asked me whether I could breathe, and, although I couldn’t expand my chest normally, I thought I could get enough air into my lungs by exaggerating the action of my diaphragm. (As I am analyzing the experience as I write, it occurs to me that this means that my chest is still bigger than my belly – so that post-Army beer gut I’ve developed could be worse!) By this point I was starting to realize that thirty minutes was going to seem like a really long time, but what choice did I have? I told them I was going to be ok. My face was pressed hard against the inside and against my arm, which was also barely fitting into the tube, and I opened my eyes, reconsidered, then tried again a few times. Although I saw material for a possibly interesting introspection about the true meaning of claustrophobia, it just didn’t seem like the right time. I kept my eyes shut the rest of the time.

So I was prone, physically compressed, unable to move, having to breathe deliberately, and aware that I would not only have to try not to fidget, but I was consciously suppressing a newly discovered (or acknowledged) fear of confined spaces. Not my definition of comfortable. And we hadn’t even started yet.


Posted by Greg as General Science, Melanoma, Posts About Me at 15:46 PST

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Wednesday, May 17th, 2006


I heard from my oncological surgeon on Monday. The report had come back from the biopsy of the lump in my chest (finally) and the results were – inconclusive. He told me my options were to attempt another biopsy with a larger needle, or to just go ahead with a surgical removal.

At first, I didn’t see the point in another biopsy. With my PET scan results having shown no hyperactivity, I thought that malignancy had been ruled out, so only the lump material was going to be be removed. They could test the lump itself to identify it. Not so, says he. Apparently, a PET scan is not ultimately authoritative. I should have known that – there always appear to be exceptions in medicine. There still was a chance it could be malignant, and that would require more radical removal, so if there turned out to be a problem, a second surgery would be required. (And it didn’t occur to me until now, but a second surgery would be complicated because the first might have disturbed malignant tissue, causing cells to start spreading to other parts of my body.) I scheduled an appointment for the next day to discuss it.

Later that evening, when I thought it out, it became clear to me that it was foolish not to undergo another biopsy first. Thinking as an engineer, who won’t want to eliminate a potential hazard of small probability but major consequence with a simple preliminary test? The cost of such testing to me was only a $25 copay and a brief period of pain, and (I can’t believe I haven’t blogged about this yet) I once walked a good five kilometers on a broken foot (third metatarsal, complete fracture) carrying a thirty kilo backpack (in the rain, in the wee hours.)

So I called the doctor’s office in the morning, told them I had decided on the biopsy, and made sure that they scheduled enough time to do it right away. After all, there was no need to have the discussion and then schedule another appointment with another $25 copay!

I went in with some trepidation, starting to get anxious again after being so relieved after the PET scan, and half expecting him to pull out some gag-shop syringe with a needle the size of a drinking straw. But he examined me first and then stopped. The lump had gotten significantly smaller. I hadn’t noticed, because I had stopped feeling it up every day after I got the PET scan results. It changed everything, he said. Now, it was clear to him that the lump was a lymphedema – a backup of lymph fluid, full of fats and complex proteins, caused by the removal of lymph nodes in my armpit, and it appeared to be going away by itself. He’s putting me in for an MRI to confirm the diagnosis, but he seemed very confident. So – no surgery for me!

Posted by Greg as General Science, Melanoma at 23:29 PST


Monday, November 21st, 2005

Working with DICOM Files

I was having problems working with digital files that came with my PET scan. A little research revealed the existence of the DICOM standard for medical image files, and I found many free DICOM image viewers, but although I downloaded at least four different viewers, I couldn’t open any of the files on the cd I got. Most of the files did not have extensions, so I was guessing at which ones were the images, but some of the files that contained useful information when opened with a hex editor showed DICOM standard headers. (My favorite hex editor used to be Hackman, which is really a complete disassembler/reverse engineering suite, but I found a much simpler and faster hex editor function in my PSPad text editor, which I use to write generic code.) I also noticed that several files had JFIF header info after the DICOM headers, and in accordance with the “Quick and Dirty Tricks” section at David Clunie’s site, I stripped off the DICOM header info and should have had a JPEG image file, but none of my viewers, including the regular image programs IrfanView and Gimp, could open these files.

[UPDATE: Found one! Try Medirec – I’m having trouble opening the raw files (don’t know if that’s a problem with the DR Systems files, or the viewer, or me), but by stripping out the header info and saving the result as a *.jpg file, I have a 12-bit greyscale lossy jpeg that I can open in this viewer – in Windows.]

I started reading up on the DICOM standard and the DR Systems compliance document, but that bogged me down pretty quickly. So I sent off an email to David Clunie. With his permission, here’s his answer:

Hi Greg

I took a look at the files that you sent, and there is nothing seriously
wrong with them with respect to anything that might confuse a viewer.

The problem you are having is simply that the images are encoded
using the 12 bit lossy JPEG transfer syntax, and many viewers just
don’t support that. Further, if you extract the JPEG bitstream,
most consumer image viewers won’t support the 12 bit JPEG form
as opposed to the usual 8 bit JPEG form either.

The bottom line is that you either need to use a viewer that
handles the JPEG DICOM transfer syntaxes, or find a way to
have the DR Systems CD creation tool encoded them uncompressed
(even if they were stored in the PACS compressed, which is
likely with that system).

I would also point out that lossy compression of PET images is
probably not cool from the perspective of quantitative PET
measurements (like SUV), though the likely error, if any, would
be very small.

That said, the images are not strictly compliant with the standard,
probably as a result of them being inverted and squeezed into 12
bits rather than 16, but I doubt if that has anything to do with
the problems that you are seeing:

% dciodvfy 196
Warning – Optional Type 2C Conditional Element=<patientposition> Module=<generalseries>
Warning – Unrecognized defined term <ring> for attribute <field of View Shape>
Error – Unrecognized enumerated value <monochrome1> for attribute <photometric Interpretation>
Error – Unrecognized enumerated value <0xc> for attribute <bits Stored>
Error – Unrecognized enumerated value <0xb> for attribute <high Bit>

I suspect that the errors are being introduced by the DR Systems
PACS, and not by the Siemens ECAT system.

If you want me to recommend a particular viewer, I would suggest
Osirix, which does open these images just fine (I tried it), though
you need a Mac to use it. It has nice 3D.

If you want to just uncompress the whole lot so that you view
them with an “ordinary” DICOM viewer, then you could try the
dcunjpeg script from my dicom3tools, which depends on the
presence of the Stanford PVRG JPEG codec, both of which are
available on my web site – but these require a unix system
on which to compile them and may be more trouble than it is


First off, I just wanted to give a big public thanks to David, who responded quickly and was very helpful. I started searching for a free image viewer that could handle the 12-bit lossy JPEGs, but haven’t found one yet. There are some commercial medical image reading programs that start around US$4K (!!!), but that’s a little more than I would be willing to spend. I noted that handling 12-bit images are planned for the Gimp 2.4 version, and I’ll be eagerly waiting for that.

Looks like I’m going to have to get back to working on my Fedora Core 4 installation so I can try David’s uncompression scripts, not to mention completing the build my other computer, which is intended to be a Linux-only box. **Sigh**. Why do I get so many interesting projects building up when I have even less time to spend on them?

Posted by Greg as General Science, Software at 05:32 PST

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Thursday, November 10th, 2005

Full PET Image

I created and posted an animated gif of the upper torso portion of my PET scan, but it’s pretty big – 5.5 MB. I’ve put it on a separate page so it won’t unnecessarily slow down any visitors. If you want to see it, it’s at 2005 PET Scan. I’ve also posted some details about my diagnosis and treatment.

If you found this page because you’ve been diagnosed with malignant melanoma or know someone who has, I’d be more than happy to answer any questions about my experience. I know that when I was first diagnosed, I was starved for information.

Posted by Greg as General Science, Melanoma, Posts About Me at 08:09 PST

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Wednesday, November 2nd, 2005

Cancer Survivor

While I was gone in Illinois, a cd showed up at home for me. It contained the results of the PET scan I took on October 21st. PET, which stands for Positron Emission Tomography, is this very cool (and very expensive) procedure where you are injected with a sugar, fluorodeoxyglucose, that has a radioactive tag, in this case fluorine 18. You sit in a quiet spot for 45 minutes while the sugar is dispersed through your blood stream, and you don’t want to move at all. The first time I did this, the technician also told me to try not to think?!

The sugar is taken up by cells that need it, and they don’t notice the fluorine atoms releasing positrons as part of their decay. The positrons – yes, antimatter, don’t get to travel very far until they meet an electron and the two particles mutually self destruct, releasing energy in the form of gamma rays and in accordance with E=mc2. Since the mass of the two particles is about 1.82 x 10-30 kg, the energy released by one reaction is about 1.6 x 10-13 kg-m2/sec2 or joules – about one 40-quadrillionth of the energy in a single Tic-Tac. I got to lie on a sliding platform that slowly moved my body through the 3D gamma ray detector, and since there’s a lot of me, it took more than two hours. The gamma rays are paired, so the detector can figure out their point of origin.

Cells take up sugar at varying rates depending on how active they are – the brain, heart and kidneys are hard workers, but nothin’ loves the taste of sugar like a malignant cancer cell! So while tumor cells are noshing, the PET scan is looking for them. And here’s a sample of what it found:

The Metabolic Greg Perry

Of course, my heart damned near stopped when I saw the big dark splotches, but it was easy to figure out heart, bladder, and brain. Finally, conclusive proof of the existence of a brain, despite the speculations of my wife, teenage daughter, parents, several high school teachers and a couple of drill sergeants.

Well, get to it, Greg! Drumroll please…

“No evidence for hypermetabolism to suggest metastatic melanoma, period”

Well, maybe the period was for his voice recognition software, but I don’t care. I have reached the fifth anniversary of my malignant melanoma diagnosis, a significant milestone, and I only had a 60% chance of getting this far. Melanoma is pernicious in that a single cell can apparently hide out or reproduce at a very low rate, and when you thought it was gone, it can decide to pick a nice spot in another organ and start making tumors. I have a lifetime ban on giving blood, and I can’t be an organ donor. But the most dangerous time for reemergence has now passed, and with continuing improvements in detection and treatment, my prospects of dying from something else, and hopefully a lot later, are just getting better.

So I’m feeling really good about this. At least until the nuclear medicine people get the payment from my insurance company and turn around to hit me up for the rest.

I’m also dying to find a 3D reader for the files on the cd. The software that the medical office sent barely meets the HIPAA requirements for providing patients with copies of their records, but the raw data files appear to be stashed away on the disk. They stripped the file extensions off, but a little peeking has already identified the file types, and there seems to be several freeware applications that can open them. The technician noticed me examining the equipment and asked if I was an engineer, but I already know how the thing basically worked – I was looking for manufacturer and model numbers so I could pull spec sheets, hopefully down to the level of file output. I won’t be happy until I get the full 3D information – maybe I can plug it in to some animation software. I hope the bones and joints are discernible – I’ll need that to accurately replicate movement. The resolution of the full scan results (I was able to get the tech to show it to me after my first scan), ought to be just incredible – way more than the image above suggests. The major limiting factor in accuracy should be how still I was able to stay.

Posted by Greg as General Science, Melanoma, Posts About Me at 10:11 PST