good vs. evil

From BOS_webalbum

by order of pseudo-consequence
sucks: my mybike kind of sucks.
doesn't suck: i can't complain about the price/bike quality ratio.
sucks: people knock over locked bikes and don't pick them up. the bikes' owners don't notice.
sucks: Boston parking usually requires bumping cars in front and back, and apparently also bikes parked too close to the side.
sucks: bike wheels get bent when people run into them while parking.
sucks: riding a bike with two extremely bent, wobbly wheels.
sucks: walking
doesn't suck: free maintenance on my bike for the first year.

sucks: spending all your time at work doing boring, probably inconsequential work.
doesn't suck: feeling no qualms for being late from lunch.

that's the story of my life.

Hitsugaya gains serious cool points in Bleach104, if not tactfully...

naruto character

Which Naruto Character Are You? Test by naruto - kun.com

gentle fist, bitches. kinda wished i could be kakashi, but i'd have to say i was a loner. still...

what I actually do.

So in this post, I'm going to actually describe one of the things I do here, since it's so hard to explain without a picture. Above is just a screenshot from one of the desktops that I'm using exclusively to draw the amygdala and hippocampus on the left brain (I'll do the right side later) of some dude who may or may not have VCFS, AKA deletion 22q11.2. >30% of people with VCFS end up with schizophrenia. Hence my lab's interest in the topic.
The boring part: First, I have to use a million different scripts and programs written by the same people that wrote the program you see filling up most of the screen above (Slicer, www.slicer.org). These take the original scan, compress it so our network doesn't overflow, move the different parts around so they are in the same space, segment and measure out the volumes of grey matter, white matter, cerebral spinal fluid and other less relevants stuff. Then we manually edit this to get an accurate measurement of the entire intra-cranial contents, which we will use to make sure that when we compare e.g. hippocampuses between people that we're comparing the volume relative to the brain size. Otherwise, extremely large-headed men would all seem geniuses etc.
Then I realign the image so that the mid-saggital (between the two hemispheres) line is straight coronally (top right and bottom right images at different zoom levels) and axially (top left image), and also that the brain is "straight" between the anterior commisure (AC) and posterior commisure (PC). These are marked for your viewing pleasure with little pink dots on the saggital (bottom left image) view. There's a lot of tricky bullshit that goes on with this concerning voxel (volumetric pixel) dimensions, and the main purpose of what I'm doing now is to figure out the best way to do this for the brain structure I'm measuring.
Then I literally draw the amygdala and hippocampus according to a relatively strict set of rules that have proved reliable and moderately valid over time in our lab. In the top left image you can see an axial slice of the amygdala (in orange) and the hippocampus (in blue). The line between them is arbitrary. They actually overlap, but for reliability purposes we include a little of each in the other. I actually draw it in the coronal view (top and bottom right), where the main instruction is literally to color between the lines (the lines being white matter tracts and CSF).
The fun part:
Eventually, we'll get to measure this and find out if the amygdala and hippocampus in VCFS patients are similarly affected the way schizophrenic patients are, we'll check to see which neuropsych, clinical psych, and psychopharm stuff it correlates with, and we'll also be able to see if this correlates with the 30% of these patients that are schizophrenic. Finally, (I think) we'll get someone else to do microarray analysis of our patients to see which genes correlate with which of these differences. Cool huh?
Also, since I'm the official amygdala-hippocampus drawer, I'm also heavily involved in determining what protocol we will use in this and other studies. The OpenOffice Calc (basically Excel) window to the right is a huge spreadsheet showing all kinds of crude difference measures between different types of drawings. Eventually, this will all get fed to SPSS, a statistics program that will chew it up and spit out the reliability, but until then I can easily modify my technique for the better using mathematical trickery like subtracting the left from the right and comparing percentages.
What you can't see is that, because this computer's moderately bad-ass and it's running Linux, I have four other desktops open, each doing something. This one is checking e-mail, reading today's words of the day, paying my credit card bills, and keeping my Google Calendar. Next door we're listening to Of Montreal Sunlandic Twins. Next door to that a perl script that one of the CS people wrote is creating .iso images and creating a detailed log of a backup project for me. etc. etc.
So, that's what I do - stare at a computer screen all day, color pictures, check my e-mail, and run various scripts with various programs. We also have meetings sometimes. And lots of lectures and seminars to help us learn exactly what we're coloring. I'm also database manager, but that's another story.
Any questions, ask my boss, cause that's all I know.

creepy

who knew rasberry shisha could be so gory?

Rasputina w/ Primus

Apparently, Rasputina is now touring with Primus. I knew that Primus was here this Sunday (at the Orpheum where I saw Decemberists, nonetheless, which is an amazing ante-bellum symphony hall turned rock venue), but I have seen Primus three times and I don't really like their new stuff. The tickets are $35. Damn. I guess I'm probably not going, but I think it would be an intense show. Ok, done venting my frustration.

What I reallly do.

sweet huh? This is basic fiber tracking of some dude's brain from the left side. This picture really has little research application, but everyone knows that pretty pictures sell grants. Seriously. So, I plan on taking pictures of the workplace and posting them so you can see what I actually do. Maybe I'll do that Friday when no one's here (except for me and a couple other RAs). I have a very intense work day here. I show up, I put my bike up, my coats on the rack, and my bookbag underneath my desk. After taking out and arranging my coffee and nalgene, I proceed to check e-mail on my three active accounts, check my google calendar, read 'words of the day' from three different dictionary sites, and finally get up, say I'm tired, and walk around to stave off exhaustion. After that first hour, I generally end up opening up Slicer, our locally developed freeware brain imaging tool, and processing things for a while. After a while, I'll remember something I was supposed to do or someone will tell me to do something involving the database. This means turning on the Windows computer, walking around and staving off exhaustion while it boots up, opening up all the same applications on it and rechecking my e-mail, and then opening up Access and Excel to modify or check the database. Most of the actual work is with Access or Slicer, and I don't feel like going into detail about slicer now, but if I ever get invested heavily in one project, I'll probably describe it here (with pictures). Anyway, that's enough writing for today. I'll let you know the enthralling details of the rest of my work day in a later post.

Bleach 101

So much better than Naruto right now.
Just wanted to say, the cello solo when Ishida's battle scene starts rocks.

what i do

is bake cookies.

apple picking in nearby MA

the scenery was infinitely better than the apples themselves. gives me some faith in my local grocery store that their apples are as good as those on the nearby trees. i do miss peach, blueberry, nectarine, strawberry, rasberry, blackberry, etc. - all the other southern, pick-able fruits that would taste so much better south of the Mason-Dixon.

expensive apartments in boston look like this.

i know, you don't have to tell me. our apartment is pretty sweet. roomy and well decorated. color coordinated, mood-lit, and trendy. I just can't help it.

Halloween, etc.

So I guess I'm pretty bad at this blogging thing. It's been a long time since my last post. I need to get myself a digital camera so I can take random pictures of things and make fun of them. At least, that's my impression of what a blog should be, given the only other I've looked at is Mike's. I need to find Matt's blog. Anyway;
So, in case no one else noticed, yesterday was Halloween. The beautiful face you see on the left is the product of a pumpkin party at one of Laura's co-workers' place out in Medford. It was a beautiful, even inspiring addition to the apartment, and it fit perfectly on the sill of the big ugly windows in the living room. The pumpkin kept the fire from lighting the 'shades,' and the smell was great. That is, until an army of diversely colored fungi grow like brain tumors and dental bacteria. Sadly, he (it looks like a he, right?) had to be taken out back and smashed the day before Halloween because he was smelling up the apartment.

In other news, I got to make a Catch 22 (slash Primus) reference today, which is always a good thing. We had people checking out our building to see if the hospital should give us more space. Bossman, who is actually a woman, said that we should make it look like all the space was filled up, so I put a nametag on the chair at the computer that I sometimes use with the name "Mudd" inscribed on it. If you don't get it, you should read Catch 22 again, cause it's great.

In international news, the French dude in our office decided we needed a coffee maker. Apparently, his persuasive abilities are at an incomprehensibly higher level than mine, because he's convinced bossman to buy a $700 coffee machine. I can't tell if this is going to be one of those piece of shit machines you get coffee from each morning along with a stale croissant in hostels in southern France, or if it's some badass drip/cappuccino monster that will make my eventual transition to barista-hood even easier. I was very flattered when my co-workers nominated me as office barista. Forget the fact that that makes me the office bitch. I need the practice.

Ok, so anyway, I've been rambling. The coffee maker thing is pretty funny though. Crazy bossman. She's so careful with money, but sometimes she just goes crazy. I wish I had 'discretionary funds.' Right now, the funds at my discretion are the 'funds that are supposed to be for grad school.' Whatever.