Saturday, June 30, 2012


Alright. It's been a lousy week overall. The migraine stuff was fun, but a distraction. Proposal failed. Barely managed to start work on what I was supposed to start at the beginning of the week. Actually, kind of a typical week. Also, my Diablo III hardcore character died, basically because I forgot to turn the video card on. So I am not playing that game anymore, ugh.

I'm downloading files for doing the driving-vid binocular rivalry experiment to my laptop now, so I can work on this at home. Must have data on this thing by the end of the week. I am optimistic, but I should have been here 3 days ago. Blame the migraine.

Really, the main reason for this entry is that by making it, I have 13 entries for the month of June. That's an all-time record for this journal: April 2010, when I was making all those internet posts, I was at 12, and May 2010 was 11. Technically that was my peak posting activity, though most of those entries were short "look what i saw" sorts of things. Most of my entries for this year, since I decided to double down and regenerate my writing skills, have been semi-substantial. I'm trying to get fluent again, and I think it's kind of working. Hopefully we'll take off from here.

Yeah, that's a plot for this journal (I am strenuously avoiding using the word "blog", though I fail now and then. I am intermittently succeeding at replacing "post" with "entry"). I have plots for everything. Abscissa is year, ordinate is number of entries. The blue markers are just counts; the red line is a 'recent activity' smoothing, just an exponential decay function applied to the data. I'm not going to analyze it here. Combined with my memory of time and place, it speaks for itself. Too bad you aren't me.

Thursday, June 28, 2012

priorities, summer 2012

augh... so bored... let's do a post on what i'm supposed to be doing right now, that i'm not doing: yes, it's time to catch up with the priority worksheet!

yes, i've been keeping it up to date every month or so.

there it is. the CI manuscript (MS_Class) is with E* right now, so i have a couple of days i could be devoting to the equivalent priority: ProjADI. but i don't want to do ProjADI. i am depressed about my failed fellowship application and all i want to do is work on modeling my stupid migraine auras, which is not what i am being paid to do, and which, as far as i can tell, does not promise to reveal anything sufficiently new or interesting to warrant spending my time on - i.e. unless i actually do start collection of real psychophysical data on that, it's not publishable. and, it's not on the priority list. migraine modeling has a priority of 0, do you hear that?

the next highest priority is ProjPrism, which i should get on with before all my subjects have moved on to other places. that's going to take some creative programming though, and i don't have a good idea yet of just how i'm going to do it. i really need to go and just sit down in the lab and figure it out. but i'm depressed, so that's my excuse. instead i'm here looking at the internet and writing a stupid journal entry on what i should be doing.

one more thing:

there you can see the evolution of my priorities over time. i do think this system is helpful in my evaluation of my projects. i do seem to be kicking off things with high priorities, though nothing has officially dropped off the list yet. waiting for reviews on two papers (MS_class and MS_blur); if those go okay, then maybe they can both be off the chart by end of the year. maybe MS_class, too.

Projs, though, need to get Projs moving. just sitting there. you're just sitting there. get up. go to the lab. go. go go go.

Tuesday, June 26, 2012

scintillating scotoma 3.a

I went ahead and figured out how to do the cortex transform. there are many papers describing the equations; some good recent ones (like this one) which are basically reviews at the same time that they are tweaking one or another aspect of the basic model. It's not really that complicated; the log-polar transform is very similar, except that the angles are calculated outside the logarithm. The space-V1 transform is the logarithm of a complex number representing the spatial coordinates plus the limit of the foveal confluence. The paper I linked above describes what further steps can be taken to get the transform more precise, accounting for meridional anisotropies. they go further, but I stopped there. The basic model was proposed by E.L. Schwartz in 1977, and hasn't changed much since then; I'm using Schira et al's version with their shear equation, and some parameters they cite in another paper.

This is similar to the second plot from the last post, but you will notice the geometry is different, as it gets narrower towards the fovea (lower part). Colors indicate time in minutes as shown by the colorbar. The grid drawn in the background isn't labeled, but it's easy to understand if you've seen these before. The lines going up and down are, from left to right, the superior vertical meridian, the left superior 45 degree meridian, the left horizontal meridian, and so on. From bottom to top, the left-right lines are spaced 5 degrees of visual angle apart. You don't see the first one until about 30mm up. The origin in this plot, (0,0), is where the foveal representation converges with V2 and V3, the foveal confluence.

This is interesting, the foveal confluence. I probably had heard of this before and forgotten it. I actually stated to E* yesterday that I didn't know what was on the other side of the foveal edge of V1, though I knew that the edges are flanked all the way around by V2. In fact, V1, V2, and V3 foveae all meet in the same place. This is apparently a relatively poorly understood region of visual cortex; imaging and physiology studies have focused on the more peripheral regions. The reason is that it can't be certain of what is being studied if one looks closely at the confluence, since the three areas are mixed together in a fashion that is still not well understood. I'm going to read more about this (the main writing on it is by the same group as the paper I cited at top; this one explains things up front).

Okay, so that map. What can I do with it, now that I have the coordinates right (or as close to right as I can)? Yes: I can measure the rate of progression of the wave in cortical distance over time. Awesome. I don't have the best method worked out just yet, but here's my approximation, summarized in the last figure below:

On the left, we have the same coordinates as in the figure above. The plotted line is the mean, over time, of the recorded scotoma regions. This is not a great measure of position of the waves, since as they got further out and larger, I couldn't trace them completely, and because it took time to trace them, so at a given epoch a trace might be in one place, or another, and that shows up here as a back-and-forth wave, on top of whatever sort of limiting bias is imposed by the screen size, etc. Still, it's okay. We know this because of the next plot: On the right, we have the distance of that waggly trace (from its starting point near the bottom of the left plot) as a function of time. A straight line. That's not why we know it's okay; it's because of the slope of this line: 2.76 mm/min. This is extremely slow, but exactly in the realm of cortical spreading depression. Not going to give references on that (need to save some work for an actual paper on this business), but they're there. Pretty sure I'm doing this right.

Monday, June 25, 2012

scintillating scotoma 3

another event is now shimmering its way out into my far left periphery. i used the dynamic perimetry program i had written; seems to work. some improvements can be made; need to include warnings or preventions for the cursor going out of screen. should implement cursor size info/adjustment. maybe cursor color or shape.

i mention the last two because definitely, there is a general sort of aftereffect. it's scotoma-like, but with no clear location of the scotoma; i.e., it feels like things are missing, e.g. if i put my hand out about 15-20 degrees left, stuff just feels kind of scrambled. actually, there is definitely a blind spot about 30 degrees left, i just found it. this is too far to measure with this screen; perimetry stops at ~20 degrees, i guess.

again, i don't know what the precursors were. been depressed all weekend (see previous post); saw some funny spots yesterday, and got preoccupied with some really visible floaters yesterday afternoon at tkd, which is probably unrelated. seems like the main indicator is just a superstitious feeling that "i wonder if it's going to happen again". maybe that's the CSD running through my frontal lobe somewhere.

note that i'm basically having a monthly period: the first of these (that i recorded here) was April 24, then May 28, and now it's June 25 (24).

i've been meaning for a while to list the other occasions that i can remember. i may be able to remember them all. before these past three, it happened twice earlier this year: once was during, uh, sex, which was weird, in China (within a few days of new years), and the second was on a sunday afternoon in late january or early february, when i was on my way to tkd, walking around cleveland circle.

before that, probably have to go back a year. it's happened several times with me just sitting here at my computer; probably half the times. i announced a few on facebook. i woke up once, early last year, with the SS starting right off. makes me wonder if it happens sometimes when i'm sleeping. it's happened after sex a couple of times. only once in the lab, i think, after j** checking my eyes. except for that morning one, i think it's almost always at night.

i would guess that, all together, this has happened 10-15 times in the last 2.5 years. until now, i don't think it had happened in summertime, only winter and spring. lots of headaches, maybe biweekly on average, without interesting symptoms.

i think these map data will be usable, and better quality than the paint drawings. not as pretty, but i can just generate post hoc pictures. i'll process them in the next couple of days, probably tomorrow. basically, it seemed very similar to the last two times, except that after the first minute or two of scotoma (again, i noticed it had started because, suddenly, i couldn't read), which i managed to record, the scotoma disappeared, or at least i couldn't find it. i thought maybe i had scared it away, but then it returned, right on track. anyways, update later when maps and stats are done.


some plots: sorry, didn't label any axes. descriptions accompany each:

This is the progression in spatial coordinates. color represents time in minutes, which you see in the colorbar. i also tied marker size to time, to help represent the thickening of the scotoma with time. 

This is progression in logpolar coordinates; x-axis is degrees from leftwards (in the last post, i was coding angle relative to 'up'), y-axis is log(degecc + 1). now it looks a lot more like a straight wave, though there is a bend to it, as if the wave has a 160° trailing angle. maybe that would be straighter with a more realistic cortical space transform? maybe not. i'll get around to finding out later this summer.

This last one is just binning the previous plot into 10° strips, plotting logecc+1 against time (like in the previous headache post). if i assume that the speed of the wave is closest to the fastest estimate that i get from these kinds of fits (it must be faster, since i'm only measuring at an angle to the wave), then i estimate that for this event, the speed of the wave was at least 0.248 logecc+1 / min. this compares with estimates of 0.250 and 0.258 for the last two events (i cited a lower number last time; that was the median, this is the max). once i learn to transform logpolar into v1 coordinates, i'll bother to do the extra geometry to measure the true transverse speed of the wave.

Sunday, June 24, 2012


okay, so, that grant i applied for? failed. not discussed. not.. even.. discussed.

so, that's disappointing. hit rate was just 10-15%, but i felt like i had something. i've seen others with the same fellowship, and i don't think what i was proposing was of any lower quality. maybe a bit further from the norm, proposing things two steps from what anyone had done before - probably better to go one step at a time. there's also the fact that i'm obviously an underachiever. i can't hide it anymore - CVs don't lie. an underachiever with an abnormal proposal.

hurts my feelings, i guess. how can it not? well.. like i've been telling everyone, as a preemptive defense, i knew i wouldn't get it. a long shot. but it wasn't some self-fulfilling bullshit. i did my best. there's good stuff in there, and i'll do it anyways. but not putting it in the top half, not putting it on par with the rest of the proposals. that does hurt. i was hoping for a rejection despite a good score.

i think i'll probably still get comments back on it. i think. d** got comments even when his wasn't discussed in the last round.

let's rephrase the bit about being an abnormal underachiever. how about.. outsider?

let's get romantic.
tell the truth.
you see yourself as an outsider,
don't you?

i don't do it on purpose.
i don't try to be on the outside
in order to satisfy some requirement
that i've set for myself.

it's just what happens.
it's what i'm drawn to.
i'm drawn away.

you make choices
that put you on the outside.
your mentor is an outsider, and
you are the outsider in the lab.

in groups of friends,
i am the one who isn't
part of the group,
who tagged along,
happily accepting all invitations.

the underachiever.
the one you don't know.
i reject what they accept.

always the quiet one.
the different one
who finds himself in strange places.

it shines through
even in an NIH fellowship proposal:
you are a risk.

yeah, screw you. i wrote all that. i wrote it, then edited it into a poem. it's because of my self consciousness, not in spite of it. i am afraid to confront what i am, but i just did it. fine, i'm mad, and my feelings are hurt. i'm a pretentious kid. i'm used to it.

have to get used to this, kid. i hear there's a whole career of this ahead. have to keep writing these things and sending them in. some will succeed, some won't. i'll keep doing what i want to do, this is my guarantee.

Monday, June 18, 2012


why would a process vary with the square root of wavelength?

with constant bandwidth, e.g. receptive field area will vary with the square of frequency (of wavelength). the linear size (radius) of the r.f. will vary directly with wavelength. a process in volume would vary with the cube of wavelength. how do you go backwards from here?

okay, so the inhibitory inputs are all squared. i want the weights on these inputs to be proportional to the square root of filter wavelength. i could get a step closer by making the linear inputs proportional to wavelength before the squaring, which changes the question to:

why would a process vary with the inverse of spatial frequency? in my mind, the weights are still tied to the size of the r.f., so that the bigger it is, the more inhibitory connections it has. strictly speaking, this would make inhibition vary with the square of wavelength.

a bigger r.f. would have more inhibition, then. i am just making this up. so, an r.f. that's twice as big would have four times the inhibition. fine, but then why wouldn't it have four times the excitation? they would balance out. but maybe the excitation isn't balanced. maybe excitatory inputs are sparser and sparser for larger r.f.s. is that true?

if it's true, then effectively the gain for different wavelength r.f.s should increase with frequency, because the density of excitatory inputs should increase with frequency.

i feel like this is getting somewhere... atick and redlich, brady and field... somewhere in there...

Saturday, June 16, 2012

stupid lazy

Alright, two posts in a row of me admonishing myself. Publicly, in theory. In theory, this is more embarrassing than it actually is.

It's Saturday evening. I have done nothing all day. Nothing. Played a computer game all morning. Read the front page of the WSJ. Ate a bowl of noodles and drank a pot of coffee. Played some piano. Looked at lots of funny gifs. Tried again to get Endnote properly installed on this stupid computer, and failed. X.0.2 + Office 2007 + Windows 7 = not work.

I have that SID manuscript open. I need to clean it up, add in those two other references I found but haven't really read because they look really dull. They're just 'relevant', in a parallel sense, but nothing obviously consequent. That's what led me into that stupid Endnote cul-de-sac again. I can do it remotely, so what. Just now I opened up the For Authors page on the journal site.

The CI paper is fine. Adding the MTF into the calculations didn't have as big of an effect as I expected, or hoped. Scaled filters are pretty resilient.

I haven't studied Chinese much in a while. I could be doing that.

No, no. God dammit. SID paper. Finish the goddam paper and upload it. There is no excuse. The paper is finished. Send it in. Dammit. I hate you.

Thursday, June 14, 2012


morning, myself. heart.
end. voice. nightingale?

This is just a diversion. There are things in life, every day, that we want to reach out and touch, or interact with, or follow, or watch, but we can't, because there are other things that we have to do instead. Other things that we should do instead. Self control can be suppression of the self, but sometimes it is just being rational, maintaining normal, keeping things the way you want them. Your mind is made up of many different parts which, on their own, are not as intelligent as you are. They don't have the same priorities as you. They don't even have the same memories as you - some of them have only existed for a few days, or months, or years. Maybe, some of them, you can remember when they came into existence. You can remember, because you are the one governing the rest, corralling them. You have to choose, at these instances, what to do - even if these things in life are like lures, and you see that between you and this other possibility, even just what ultimately would be a fleeting bit of soon-to-be-nothing, is a transparent membrane of a single impulse.

It's just a diversion. Maybe don't go back there. Maybe come back here, and see what you did, to keep from going there. Remember what there is in other places. Keep things level. Life is hard.

Wednesday, June 13, 2012

monitor MTF? sure!

Okay, so I need to know the spatial frequency transfer function of the monitor I've used to do most of my experiments over the past couple of years. I've never done this before, so I go around asking if anyone else has done it. I expected that at least B** would have measured a monitor MTF before, but he hadn't. I was surprised.

Still, B**'s lab has lots of nice tools, so I go in there to look around, and lo, T** is working on something using exactly what I need, a high speed photometer with a slit aperture. So today I borrowed it and set to work doing something I had never done and didn't know how to do. It was great fun.

D** helped me get the photometer head fixed in position. We strapped it with rubber bands to an adjustable headrest. I've started by just measuring along the raster. The slit is (T** says) 1mm, which is about 2.67 pixels on my display. I drifted (slowly) squarewave gratings with different wavelengths past the aperture - this was more complicated than it sounds. The monitor is run at 100Hz, and CRTs flash frames very rapidly, just a millisecond, so getting the photometer settings just right (it runs at 18Khz) took a bit of adjustment, and figuring out good settings for the gratings, slow-enough speed to drift them at (I'm limited by the 10 second block limit imposed by the photometer)..

Anyways, I got back temporal waveforms which I treat as identical to the spatial waveforms. As expected, the power of these waveforms drops off as the gratings get finer. But, I know that it drops off too fast, because of the aperture. If the aperture were exactly 1 pixel across, and if it were aligned precisely with the raster, and if a bunch of other things were true, then I could know that each epoch recorded by the photometer reflected the luminance of a pixel, and my measurements would reflect the monitor MTF. But, like I said, the aperture is 1mm, so each 10ms epoch is an aliased average over >2 pixels. I'm not even thinking about the reflections from the photometer head (there's a metal rim to the aperture T** had taped on there).

My solution: code an ideal monitor, record from it with the same sized aperture, and divide it out of the measurements. I can then guess a blur function - Gaussian - and fit that to my (4) data points. That's what I did: here is my first estimate of the vertical MTF of my Dell p1130 Trinitron:

The Nyquist limit for this display, at the distance modeled here, is about 23cpd, so I guess this Gaussian is in about the right place. It's hard to believe, though, because horizontal 1-pixel gratings look so sharp on this display. I feel like these must be underestimates of the transfer. I am nervous about how awful the vertical will be...

It wasn't too bad, just a bit blurrier than the horizontal. Still makes me suspicious that I'm underestimating the horizontal. Not going to bother putting up plots, but here's my estimate of the pixel spread function (you can just see that it's a little broader left-right, that's the vertical blur):

Thursday, June 07, 2012


internet post!

So, earlier today, I got an email from the "Security Operations Lead" at NASA Ames, saying that a whole batch of people's passwords and account names had been accessed. I had an account there for a meeting I went to earlier this month; coincidentally, immediately after attending that meeting, I noticed that one of my peripheral email accounts had been accessed, and at the time I blamed it on the hotel.

Just now, I get an email from something called Zimbra, informing me that:
You requested your Email Account  on June 7, 2012 at 11:02 PM CS to be deactivated and deleted from a location in with this IP number;
2. Click on  ( cancelrequest) to cancel this request; else your email account will be deactivated and deleted within 24 hours
The sender's address was "". Yeah. Zimbra is apparently some sort of open source email server software for Linux machines. So this doesn't have anything to do with Zimbra.

The IP address leads to a machine in Mexico, with the URL This machine seems to have all ports open, i.e. it's either a totally open proxy server, or some sort of disguise for something else.

That URL to '' was actually an alias in the email (no I did not click on it, I am not stupid), for "". From their website I can't tell what the hell contactme is, but it looks their site was probably co-opted. I wonder what's there...

Anyways, the relationship to the NASA thing is just coincidental timing, but makes me a bit paranoid.

*edit 6-19-12*
Got called down to to the network office this morning to change my password; apparently the NASA thing had gotten distributed to everyone whose ids were leaked. The admin forwarded to me the info he'd gotten through the Harvard IT director, and based on that I found this:

who knows how long that link will stay alive. anyways, it's a list of the email addresses, but no passwords, for everyone that attended that workshop.

the header on the document:

Join me on twitter :!/bzyklon

Author : ZYKLON B
Target : NASA Ames Research Center - Ocular Imaging Laboratory (
Reason : Curiosity, Challenge.

Note : NASA Glenn research center already hacked 5-6 weeks ago.

anyways, that's interesting. you look down the document, and there we all are! yeah, hackers have twitter accounts!

temporal friction

We came to see the problem as one of material friction, rather than of abstract entropy. Information was still the key, but it was finally clear that what we perceive as information is just the tip of an iceberg.

The resolution of the dark matter problem demonstrated that the deeper structure of reality is anisotropic, made up of tiny needles of entropy - a material structure, now, not a mathematical description. And these needles, they are all pointed towards the past. Whatever part of the universe that moves away from the past is brushed through those needles, which scrape and tear and lacerate the informational structure that we recognize as reality.

That reality we came to see as the product of a long process of selection - some informational structure is torn apart as soon as it forms, while some is hardier, even self-correcting. Life was a structure, we saw, that had adapted to a long path through the deeper universe, even making use of the dark matter anisotropies, to store and convert energy, to drive its own processes of selection and sub-adaptation. But no forms of life could navigate through the darkness. Not until the humans came, and then, for them, it became a prime concern.

We navigated the Earth's surface, its skies and its seas. We navigated the first darkness, of space, and the surfaces of other worlds. All the time, there was that constant abrasion, wearing off man after woman, nation after world, age after eon. All along, we were looking for the way through - the clear way through the darkness. We found it - as I said, we came to see the problem as one of material friction.

Moving against the anisotropy disrupts information. Moving with it smooths information, conforms it, puts it in neat rows and columns, but this has the strange effect of making life uninteresting. If you're adapted to something, then when you lose it you notice it's gone. It's the same with entropy - when you go through life with information conforming rather than disrupting, you go from senselessness to perfection. This can be beautiful, but too often it's just another level of senselessness, on top of the fact that conformative memory processes take a lot of time to install and master, and you find yourself missing the old order of things, no matter how far beyond human you've gone. To have your thoughts and actions gather energy, collect and bind heat, and deliver it into your body... a useful novelty, a tool or practice, but nothing fundamental.

What was interesting was when you could remove the anisotropy altogether. No arrow of time, except for what you choose to arrange. Laws of thermodynamics become adjustable, optional. When we learned not just to navigate through the darkness, but to engineer it to our own purposes, then...

That, more than any other development, was what changed us.

Tuesday, June 05, 2012

transit venus

SO, I had been planning to actually get my old reflector out and make a little projector to watch a bit of the transit, before the sun set today. but, it's been days since the sun was out, so I never had any chance to test anything; actually, with no way to test a setup, and with the forecast looking like it was going to be the way it was, I didn't wind up actually putting any of the parts together.

In other words, it was too cloudy to see it from Boston.

I've been watching the NASA feed of it, it's better than nothing. I think the transit will be over soon; I'll stay up as late as I can to see if I can't see the planet crossing the limb.

That picture is awesome, right? NASA again.

Sunday, June 03, 2012

sum.. sum.. summm... summation?

ok, so i'm working on this classification image paper, and it's going really well, and i'm pretty happy about it. i feel like i've got a good handle on it, i'm writing it in one big shot, the analyses are all good, the data are fine, it's all under control. i'm pretty happy about this one. i keep telling myself that, and then noticing that i keep telling myself that. i guess it's in contrast to the blur adaptation paper, which was such an ordeal (took 2 years, basically), and then the magnification paper, which just isn't much fun. i feel myself moving down that priority list - hey, i should do a post on the priority spreadsheet! i made some nice plots in there!

anyways, the CI paper, it's going well, but i'm constantly on the lookout for problems. so tonight, i finally thought of one. not a crucial, deep problem, but a problem with how i've calculated some of the modeling stuff, a serious enough problem that i'll probably have to redesign a bit of it before doing the final runthroughs. i'm writing this entry so i can just sort of kick off thinking of how to solve the problem. here it is, right plain as day in this little cluster of plots from last year's poster, which has become this fine little paper:

the problem is spatial summation - or, the problem is that you don't see anything about spatial summation in those plots. for the main models, i have a CSF that was measured using test-field-sized images. the thresholds measured must reflect a sort of spatial summation, then. the problem is, i've been using those thresholds to set the baseline thresholds for the models, and then summing over the spatial responses. i had kind of had an inkling that i was being lazy there, but had overlooked how obviously stupid that is. i haven't tested the models on the threshold tasks, but i think that they would necessarily get much lower thresholds than the humans; spatial summation should give you a lower overall threshold than you would get for any single location. i need to think of a quick way to solve this, because i don't want to wind up estimating the model CSF through simulations...

and the simulations then raise the problem of noise, and how many samples should there actually be, etc etc... i guess there are benefits to doing things the simple way first, but i think i've run myself into a weird little corner here. gonna need to talk to somebody about this, probably..