i havent eaten, i havent been sleeping, missed class a few times, and feeling sick. but… i have data. sweet sweet data. 250 lines of code in R today alone. my honors thesis will prevail

These are my MEG/MRI compatible tactile stimulators. I designed them for Ramachandran. They poke people.. very, very well. When I add my fiber optic signaling component, the data acquisition engine will log the precise time that the subject was stimulated with speed of light accuracy. 

They look so cool! Theres 2 different types of plastic so the parts don’t stick while sliding. I’d way rather continue to design all of my research instruments from scratch than buy someone else’s parts and have to hack them together. Thanks again David Malmberg for being the best engineer to collaborate with!

So this post is more of a vent than anything else. I had an essay midterm due yesterday. Today I picked up the 2 air pistons/ cylinders/ actuators that David Malmberg and I have designed over the past month from the Scripps machine shop. It has a small problem with the vent holes, but I will take care of that later this week. I got access to a small staff shop around the corner so I can now build my own parts from scratch!! (woo hoo! i new 5 years of shop would come in handy one day haha). Tomorrow I have a counseling and therapy midterm. Weds I have my first 3 subjects for my honors thesis. From here on out, I have 3 per day for the next 30 days (6 hours/day!!). Thursday I am giving a talk/seminar on neuroimaging at the UCSD Radiological Imaging Lab. I have a subject booked right after. Right now, I am ordering parts for an analog relay. I need to read about the retina for tomorrows computational neuroscience lecture.

Seriously. WHAT?

Tianna Lewis, just two years old, suffers from RAS (Reflex Anoxic Seizure) a strange evil that allows the circulation of blood to the brain when something surprising or makes you mourn.
Little Tianna’s condition is triggered by tears, because if she does, her skin turns white, the body is stiffened, and her heart and breathing stops temporarily. She was diagnosed at 18 months old, and her parents have the difficult task to prevent her from crying.
Reflex anoxic seizure reportedly can also be triggered by pain, fear, fright or a very hot or cold bath.
Fortunately, reflex anoxic seizures generally receives less frequent and eventually stop in childhood. Sometimes the attacks persist until early adulthood.

source

I am taking Dr. Terrence Sejnowski’s computational neurobiology course this quarter and the required text is The Computational Brain by Churchland and Sejnowski. I am only on chapter 2, but the book so far is a witty fusion of philosophy and biology. When I finish, I promise I’ll write something useful about it.

”[…] emergent properties are high level effects that depend on lower level phenomena in some systematic way. Turning the hypothesis around to its negative version, it is highly improbable that emergent properties are are properties that cannot be explained by low level properties (Popper 1959), or that they are in some sense irreducible […]” (the Computational Brain pg.3)

I just sent this to all the psych majors at SDSU. Its good advice and its how I got here. 

Dear Psychology Peers,

I was impressed by the (overwhelming) number of responses for my neuroscience seminar/tour at UCSD. However, I noticed that many of you are sophomores and juniors who are just starting out and want to gain exposure to the field. This sort of experience is extremely helpful in making decisions about where you want to go with your education. The best way you could possibly do this is by participating in a research experiment.

When you participate in an experiment, you get to see the real equipment and methods first-hand. You can also ask questions about them and get answers from experts. At the end of the day, you not only get to see equipment like MRIs and EEGs in action, but also see your own brain data at the end of it. A few of my friends now have MRI pictures of their brain as geeky facebook photos.

Another important reason to participate in research is that you can meet people and check out labs. It takes work to find the right lab for you —you really have to look around. The best way to see a lot of labs and actually talk to people is to participate in research experiments in many different labs. Then, once you’ve seen your options, make a decision and apply.

Lastly, if the lab or experiment is not a good fit for you, there are still several gains. (1) you will probably be paid for your time, (2) you are now sure that you DONT want to study that, (3) you can always ask the researcher where to go and build your network. 

Hope this helps!

Best,
Dave Deriso
Paulus Lab
Ramachandran Lab
davidderiso.com

Using the iPhone with External Devices and Adobe AIR

The iPhone SDK does not allow access to the bluetooth serial profile (SPP). This means that the iPhone can’t communicate with popular physical computing development platforms like arduino — making it difficult to use the iPhone as a medium for research in human-computer interaction.

One alternative is to enroll in the ‘made for iPhone’ program and install a special chip in your hardware, although the connectivity is still limited. Typically these sorts of programs have lots of red tape and cost $$$.

Regardless, the fundamental problem with the iPhone’s bluetooth barrier is not hardware. The iPhone comes with an incomplete ‘bluetooth stack.’ This ‘stack’ contains all of the files necessary for the various forms of bluetooth communication, and is missing the components necessary for serial communication (SPP) —required for using SPP based external devices such as cameras, audio equipment, or keyboards. In response, several projects have emerged to try and create a full bluetooth stack for the iPhone. They include:

iBluetooth Project

bluesn0w

sweetTooth (a GUI of bluesn0w)

reinforce labs

At the moment these options are only avaliable for the ‘jailbroken’ iPhone and offer no support. I can only hope that Apple gets its act together and creates a SPP bluetooth component for the iPhone so that I can develop iPhone devices for treatment of neuropsych populations.

The only piece of good news is that the Adobe Labs team that is releasing the new CS5 suite has developed the ‘Packager for iPhone’ that essentially converts you AIR application into ARM assembly code via ‘Just in Time Compilation.’ This gives you a truly native compiled iPhone application.

Now, if only the bluetooth stacks would talk to the AIR converted iPhone application, I could do anything. So, I contacted the Adobe developers and the response was “the iPhone SDK doesn’t even allow bluetooth access, how can we?!”   Gah!

The plan is:

1. find out how to port the missing driver file into the bluetooth stack of a non-jailbroken iPhone. (is this possible?)

2. write a library for the new adobe air CS5 packager and get it to talk to the bluetooth.

i scored a 13/22. not bad for a non CS major :)

New schedule till June 2010

The Ultimate FMRI Paper

This is a figure from the 2009 Steve Smith paper. Think of it as a paper that uses ICA to review our main findings of FMRI studies of cognition. Sounds daunting, but with a sample size of 30,000, its credible. Take a gander at the neat graph above. Each # on the x-axis corresponds to a network of brain areas (outlined in the Supplementary Info link below). The y-axis lists several cognitive proceses. The green graph indicates which networks are involved each of these processes and has a color code to indicate the % BOLD signal change seen in these networks for the respective tasks.

My response was: (1) I need to read more articles by Dr. Steve Smith, (2) we dont need to keep looking at these areas for “cognition studies,” (3) collective brain-data repostories are worthwhile, (4) review papers like these are possible now. At the end of the day, this is quite possibly the most insane paper i have ever read. I take issue with only 1 factor in such a large scale experiment —quality control. 30,000 brains/365 days = 82 brains per day or 10.25 brains per hour (assuming an 8 hour work day with no weekends for 1 full year). Who can do this without error? I love the idea, but question the attention to detail and therefore have trouble believeing the results as ‘truth’ on their own. However, since the findings do agree with previous research, I can go ahead and reject the null.

Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., & Fox, P. M. (2009). Correspondence of the brain’s functional architecture during activation and rest. PNAS, 106(31), 13040-13045.

 

Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., & Fox, P. M. (2009). Correspondence of the brain’s functional architecture during activation and rest. PNAS, 106(31), 13040-13045. 

Supporting Information