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Posts tagged fmri


I’m sitting here at the lab, waiting for the very last step in my data processing to finish.  I started with raw text files that the fMRI scanner outputs while you’re doing your business, and when this model finishes estimating, I’ll have a whole set of pictures of someone’s brain.  This is awesome.  It is also extremely time-consuming.  I’ve been working on it for the last four hours, and this is only one subject’s worth of data, for one portion of the study.  Oy.  This is why we’re trying to get this batch scripted.

Life, other than the data-processing portions, is going very well.  I acted quickly on this advisor thing and submitted to him an admission of my pipe dream project.  Turns out, he also thinks it’s cool and not impossible, and would be “happy to support this effort”.   In that he’s already given me a carte blanche for designing and running an fMRI study, and that I’m right in line to start something for my second QP… I’ve basically hit the jackpot.  It’s not going to make him any easier to work with, but it certainly makes me feel secure in my choice.  It’s nice to be listened to!

I had a really awesome section this morning, which was also a nice surprise, given how poorly this material went over in the previous sections earlier this week.  I changed it up quite a bit – had them work in small groups instead of all trying to solve the problem with me on the board.  Also we listened to The Beatles while we worked, and I thought that did a nice job of waking them up and getting them moving this morning.  9 am can be a little bit early for any kind of critical reasoning skills to be awake, so any little bit helps.  I’m definitely going to retry this music + phonology problems idea next week.

I was offered another research opportunity today which I wisely declined.  With this fMRI thing ready to plow ahead full steam (and full steam it should be, given how long this stuff takes), I just don’t really have time to dabble in other projects.  I did agree to record stimuli for this neat language contact experiment our resident creoleist is undertaking, but he understood that I was too busy to attach myself any more than that.  I did have a good idea of who else in our department would be good at this stuff, so hopefully my name dropping gets me some good karma points.

Geesh, it’s almost 5 already.  I keep thinking this thing is on it’s final rendering step… and then it’s not.  Time to go home and leave it to run?  Guess I won’t make it to my pretty brain pictures after all.

Applied me-matics

Excellently productive day?  I think so!  Though I didn’t do any reading, and a day without reading is never a great idea.  What I did get done was some prep for section, and the approval of a prompt for both my neuroscience class, and my typology class.  In fact, my typology professor had some really good ideas about what direction to take my paper, and thus I’ve even sort of gotten an outline put together for that one!  I’m hoping sections go well tomorrow.  I have to hand back the midterms, and my Wednedsay section did particularly poorly.  We’re also moving into real “discussion” territory, and these guys also aren’t too participatory when I’d like them to be.  So we’ll see how well I can manage to swing chattiness.    I’ve also been scheduled for my fMRI safety training tomorrow, so I can officially operate the magnet!

In non-school triumphs, yesterday we did our tri-weekly co-op trip, so there is actually food in the house today.   I had a smoothie and toast this morning, which is hands down my favorite (regular) breakfast.  I also made it to the gym, which is good since I skipped yoga in favor of food shopping yesterday.  I really need to get to yoga on Thursday, I miss it.  I was pretty stressed out pre-gym, and I’m happy to say that working out calmed me down.  Also, I came home and cleaned our room (which was a complete disaster) so I’m feeling pretty accomplished!  Here’s to hoping I can keep up this level of optimism for the rest of the week.

Bald me

Mondays are a good days.  Had our reading group meeting at the center which was a nice relaxing time since I wasn’t presenting.  It feels like things at the lab are getting a little more friendly, probably just because I’ve been spending more time there.  For whatever reason, it’s nice to feel slightly more welcome.  Class this morning was also excellent – a lecture on working memory that seemed to touch on some of my work, so I had lots of questions for the presenter.  Interesting stuff.

Also, I got copies of my brain images!  Exciting stuff.  The data includes the skull and skin on the skull in addition to the actual brain junk, so you can actually 3D render my whole head without my hair and see what I look like bald!  Very odd!  So I spent a while playing with my brain slices, which is much fun.  I’ll post some up later.  Turns out I’m going to get scanned again in a few weeks, and Lewis too, because the scanner messed up my data.   It was interesting, so I’m really not bothered.  My lab mate is even going to let me run the scanner while we’re scanning Lewis, so I’m looking forward to it!

Got my work done early, and I’ve been doing a good job of not working harder than I need to, so I spent the evening working on some audio files we’d recorded from our vinyl.  I didn’t even go to yoga tonight, though I would have liked to.  I did something funky to my arm yesterday at the gym, and today it really hurts to straighten it all the way so I figured it was best to rest and let it recoup a bit.  What a lazy day!

I’m thinking about hitting up Vacaville tomorrow to get some more sewing goods and maybe spend a gift certificate I’ve got on some summery clothes.  Could be good!

250th post!

Like I told Lewis earlier… today is one of those days that will probably never happen again.  Today is the day I both got a scholarship, and a brain scan!   What are the chances?   I’m pretty excited about this scholarship.  The money will be nice, though it’s not a great amount, but I feel like more importantly the outword show of faith from the department and nice CV boost are priceless.  I had been worried when I first got in to Davis with Lewis that I was perhaps an accessory to his more glorious career, but since actually getting here and starting classes I’ve felt like my work speaks for itself, and I’m showing myself to be a worthwhile asset.  This just sort of proves it, in a fancy sort of public way!  I’ve never gotten any sort of meritorious scholarship before, and it means a lot to me that this isn’t just part of some big pool of money that I got a piece of for being a decent student.  I got our department’s only scholarship – a nod from other linguists that I’m a promising student!  Yay!

So, yeah.  It was a wildly successful day, even though it got off to a rocky start.  I slept really poorly last night, and woke up pretty grumpy.  We had a great night last night, playing Apples to Apples and Zombie Fluxx with a bunch of Linguists and their significant others.  I made a chex mix-like party mix (which was really good) and a strawberry rhubarb crisp (which was tasty but amorphous) and others brough various goods.  It was originally going to be at someone elses’ house, but she got sick, so we emergency hosted, and it was a good excuse to finally clean at least the common areas in our house.  Anyway, after all that adventure last night, I just couldn’t sleep – heart palpitations and the like.

So I made muffins this morning – apple cranberry ones, whole wheat with orange zest and walnuts – and they turned out really well.  Muy sabroso.  Went to the gym after that and worked out pretty hard.  Weekends are a great time to hit up the gym since no one is there, and I had the women’s room to myself.   Worked out for longer than usual, and then I got to try all the weight machines I’ve been curious about, since no one was there to see me make a fool of myself.  Was pretty beat when I got home, but I took a real nice long shower and had some lunch and got back in the swing of things.

Ran off to Sacramento after that to visit the UC Davis Imaging Research Center, where my lab does its fMRI scanning.   I was volunteering to be a subject in the control group of  a sign language study my advisor is working on, mostly to get the chance to do an fMRI study.  Being in the scanner is hard to describe – on one hand more difficult than I would have thought, but on the other hand, also less clausterphobic and nerve-wracking than anticipated.  The tasks were amusing, and being in the magnet doesn’t really feel like anything more than being anywhere else tiny but safe while your head is strapped to a plank.  I suppose what I mean to say is the magnetization isn’t really discernable.  I was glad I had taken that fMRI class already though, because I could identify what the noises were probably being caused by, and I knew enough to know what the magnet would and would not do, and thus it was more interesting than scary.  I can see being pretty wigged out by all that stuff if you were a kid or someone without the background on RF coils and all that.  Anyway, I would certainly do it again, I thought it was rather fun.  I’m sure I’ll post a picture of my brain when the person running the study emails me a copy of some of my high-res anatomical scan data.  I’m looking forward to it!

Post-scan I was hungry and eye-strained, but happy that Lewis had come with me, and we were going out to dinner!  Hit up the Tower Cafe, where our friend Maya works, and had the most delicious dinner and wine and desserts.  Maya was even working, so we got to chat her up a bit.  It was nice, since we haven’t had a chance to catch up with her in a while.  I do hope we can do something soon, I really enjoy her company.   Anyway, came home and Lewis gave me a really nice neck rub (which I needed after that hour and a half of forced immobilzation in the scanner)  and we listed to some good jazz records.  And I got a barrage of congratulatory facebook messages in my email.  Nice way to cap off a nice day!

Poeppel & Popples

Mondays are one of my favorite days, because I’ve got my 7:30 yoga class.  Yoga at the end of the day is the best!  I come home all relaxed and feeling well and ready for bed.  Today’s class had a bit of an odd twist to it, though I’m trying to not make anything of it.  While we were doing our little cool-down meditation (where you just lie on your back and breathe) the instructor came and gave me a mini-massage – feet, knees, chest and head! – and didn’t seem to do this to anyone else.  It was a little awkward!  On the other hand, it was also very relaxing and felt nice.  I’m going to assume she was just being nice and maybe I looked like I needed some extra relaxation.  Otherwise, I’m not sure what to think!

The rest of my day was also excellent, and thankfully not also awkward!  Class this morning (cogneuro) just about killed me.  A big uppy-up was guest teaching, which actually isn’t unusual, since we usually have guest lecturers present the work their labs are doing once a week.  This one was strange because this guy already gave his lecture, but presumably our teacher was just out of town or something today, so he sat in for a second day to oversee the student presentations that we do the other half of our time.  Sadly, a kid was presenting work this guy had published, so it took him a whole hour to get through his 20-minute powerpoint since the uppy-up had a bunch of stuff to add after every point.  Pooh.  We only had two presenters today, so we were going to get out an hour early – but we almost got out late instead!  Not to worry though, because our Wednesday class was cancelled.  Yay!

I got lunch with Lewis at a great cafe just a few blocks from the Center, so that was a wonderful find.  Gourmet sandwiches for 6 bucks!  I’m always on the lookout for good places that aren’t crowded, expensive, or crappy.  This place is friendly, delicious, convenient, and relatively crowd-free!  Yay!  After lunch I was supposed to hang out in the lab until it was time for our inaugural Journal Club meeting, which my advisor-to-be had asked me to run today.  Presented two articles there, both of which had fruitful discussions, and I think I did very well.  Or at least as well as one could expect to do in a we’re-all-friends no-consequences sort of meeting.  I’m happy with the result, at any rate, and off the hook for journal club for probably the rest of the quarter.  Whoo!  Also got myself signed up for some more fMRI stuff this weekend — one session worth of scanning shadow (hopefully we’ll be less rushed and I’ll get more info) and once to be scanned myself!  I’m hoping to come out of this with a nice high-res picture of my very own brain.  And hopefully I don’t panic in the magnet.

Only other triumph worth mentioning today is that I finished sewing Lewis’ PJ shirt!  It turned out pretty well, if I do say so myself, though I know I messed a number of things up.  There are just a handful of things that show (like the pocket which is kind of crooked), but I learned a hell of a lot, and there isn’t anything I think I didn’t learn from.  The next shirt will be mucho mas smoother.  I’m really excited to get moving on the pants so the whole outfit will be done, but I lost patience with it today after wrestling with the button holes for a whole hour and a half.

All things considered, it’s been a most triumphant day!

Just Keep Moving

Blurg.  Too tired to post, per usual.

It’s Tuesday.  It’s our first day back from San Diego.  The trip was wonderful, the train trip back home was fantastic, and I’m exhausted.   Tomorrow’s my first of my worst days – Wednesdays I teach section at 9 am, and then I have to jet myself over to the CMB for my CogNeuro class, which inconventiently starts at 9:30.  I’m really not looking forward to missing the first 45 or so minutes of class every week, but it’s only one day a week, and I’m trying not to stress about it.

I’ve been good about the stress level lately.  Went to the gym this morning and worked out for a while, which seems to leave me feeling more able to cope than days when I don’t work out.  I have no idea why that is, but I’ll take what I can get.  I also skipped my only class today (Ling 1 lecture) so I could get some sleep, cause 9 am was feeling way too early after getting in so late last night.  I also got my first trip to the Imaging Center to shadow an fMRI run-through.  It was neat, and useful, but not quite as exciting as I was anticipating.  Maybe I’m just tired.  I did get some good advice from the girl running the study, who also has worked in our lab for the last few years.

There’s a lot more I’ve missed out on blogging… but right now I’m just nervous and ready for bed so I can get through my big day (morning?) tomorrow.  I’m sure it’ll all work out fine – I’ve got a million things planned.  Fingers crossed.

collocation or whatever

I don’t like how much I’m relying on lists these days.  But I’m just so busy, and so tired by the time I get to my poor blog!  With resignation, I give you today’s list:

  • Ling 1 this morning was very amusing!
  • Did some laundry in prep for the upcoming San Diego trip
  • Decided at the last moment to hit up the corpus linguistics group meeting
  • Ran out at the end to hit the gym – good yoga today, but fast and intense.  Chatted the teacher up after class and she was very nice.  Nicer than anticipated given her class demeanor!
  • Made it home just in time to meet Heather and Kevin for a dinner out to celebrate good news for them!
  • Got an email from research professor setting up my first fMRI shadowing adventure for next Tues.  I’m really excited!

I’m looking forward to my last day of classes here… but dang, it’s been a long week.  And it’s going to be a pretty crazy weekend.  Phew.

A good word: cytoarchitectonics

Super productive day, but I don’t feel much like being expository tonight.  Mostly because I’m pooped!  List form it is:

  • Cogneuro class this morning – learned about EEGs.  Very neat!
  • Met with lab professor to set up research plan for this quarter.  Starting a Monday reading group (to count as my “directed reading”) and a Wednesday hands-on training deal.  Professor wants me to be trained to analyze the raw fMRI data he has collectd but not processed yet.  Also intend on starting a new study (to be partially directed by my interests?) and gathering pilot data already this quarter!
  • Spent a while at the gym doing generic cardio stuff (stairs, mostly) cause I think it helps destress me a bit.  Also tried an actual weight lifting device, and now my arms are sore in the strangest places!
  • Made oatmeal cookies with orange-essenced cranberries and white chocolate chips.  They turned out pretty good, for a recipe I hadn’t tried before.  Should bake them a little less next time.
  • Did a bunch of paper trolling (as in, reference chasing and google scholar browsing) for papers to start our reading group off with.  Too many choices already, but I found some really good background papers for myself at least.
  • Traced the pattern for Lewis’ PJs onto sturdier tracing fabric, and cut out all the pieces.  It’s starting to look like I’m doing something with this!

That’s all from me tonight.  This week is going crazy slow!