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Matlab / Sun grid processing PDF Print E-mail
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Thursday, 19 August 2010 15:04

At the Olin Center, we originally had a half dozen Solaris computers that we used for fMRI processing. Storage and processing were done on the same box, and data moved between servers only if we ran out of space on one. A couple years ago we got a linux cluster with 28 nodes, 8 CPUs each, and a separate 100TB storage array. The whole cluster is controlled by Sun Grid Engine and I adapted our fMRI processing to fit that.

Since we've run more than 7000 studies, with more than 30,000 functional data series, we have a lot of data to process. Automatic batch processing was the best solution. Simply, I built a system to treat the processing of each subject as a cluster job, and created a manager to submit jobs to the cluster.

This allowed us to preprocess (realignment using INRIalign) and runs stats on a batch of 1500 subjects in one week.

 
Surgical navigation PDF Print E-mail
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Saturday, 07 August 2010 18:35

I got involved in a very interesting project at work with fMRI and presurgical mapping. A couple years ago the neurosurgery department at Hartford Hospital contacted the Olin center to form a collaboration with us. The goal was to have patients who were about to undergo brain surgery to do some simple fMRI tasks to map out language, motor, visual areas before surgery. The research has two parts: 1) help the surgeon avoid removing important areas of the brain if possible 2) get information back from the surgery to see if our estimations of language, motor, visual areas were accurate. During the surgery, the surgeon stimulates areas of the brain to 'turn off' activity in those areas. If the person can no longer speak when an area is stimulated, then that area is responsible for language.

My involvement was in the second part, comparing the computed areas of activation from fMRI with the real stimulation results. To do this, we needed to get the coordinate of the point of stimulation that actually did something. So for example the surgeon identifies an area responsible for language, and we note the location of the probe on the navigation system. Originally, the neurosurgery department was using BrainLab navigation system (which they still are), which did not directly give us coordinates back after the surgery. It was my job to attempt to decrypt the output from BrainLab to get the coordinates we wanted, however the department chose to trial the Medtronic system recently. This system gave us the exact coordinates we wanted, in image space! We will see what happens as the Medtronic trial moves on.

Observing surgery was pretty interesting. Those surgeons are amazing: no sitting, eating, or bathroom for 7 hours.

Last Updated on Thursday, 19 August 2010 15:04
 
Street Maps PDF Print E-mail
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Sunday, 31 January 2010 21:27

Many projects on this site are from the past, but I'm only just now posting them on this website. This one is one of the earlier work projects that is worthy of posting online. Most of the work I did at Travelers wasn't terribly interesting. It was mainly ASP programming for internal websites and databases. But I found one opportunity to experiment with geo-location, or at least providing a list of the closest vendors to a given zip code. I found some data from the Post Office which provided latitude/longitude for zip codes and it worked pretty well, but I also found some street address data from the US Census Bureau's Tiger Line files. From this data I experimented with drawing street maps. It was common practice back in 2001 to generate web based maps, but I wanted to give it a shot myself.

After finding a source of free geographic data from the Census Bureau, I found I could make street maps with the data as well. Some of the material I created may be copyrighted by Travelers, so I've limited this section to just results of the map project.
I came across the Census Bureau's data while I was looking for a source of data from which to create driving directions. So I decided creating maps would be the best way to learn how I could create driving directions. I quickly found that it was not a good source of data for driving directions because it does not contain three important things: exit numbers, one way street indicator, street intersection data. So I stuck with making maps, hopefully for the purpose of showing a user where the vendors are in relation to their address. The maps shown here do not have street labels, which keeps them from becoming cluttered and unreadable. I also worked on methods of improving the map drawing to allow for select street names when many streets are present. When street labels are added, they follow the angle of the street segment.
View Maps in Connecticut:

06183 (Hartford, CT) 1.57MB (2600x1950)
06269 (Storrs, CT) 820KB (2600x1950)
06615 (Stratford, CT) 770KB (2600x1950)
06770 (Naugatuck, CT) 511KB (2600x1950)

 
gbookcards.com PDF Print E-mail
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Sunday, 31 January 2010 21:20

A long time ago, around 2002, I was working on a C++ project and I was looking for a C++ quick reference. Nothing in depth, but a single sheet of paper that contained all the common c++ syntax. Since I couldn't find anything, I decided to create a C/C++ reference card. Over the years I ended up creating a Chemistry 1, Chemistry 2, and with the help of some other people, PHP and Organic Chemistry cards. I got some ISBNs from lulu.com, printed the cards myself, and sold them on my site (http://gbookcards.com), eBay, and amazon. Unfortunately, the demand was so low for the cards, it wasn't worth it for me to pay Amazon for the right to sell them on their site. So I just let the venture fade away. Perhaps someday I will make the cards open-source and allow people to print the PDFs on demand.

 
Pupillary Response During the Auditory Oddball Task PDF Print E-mail
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Friday, 01 January 2010 00:00

 

I created a system for analyzing pupillary dilation in a similar way to the way event related potentials (ERPs) are processed. I did a group analysis using the Fusion ICA Toolbox developed by Vince Calhoun with 19 subjects who completed the auditory oddball task while simultaneously collecting pupil diameter information. The analysis was accepted at the CNS 2008 conference.

This study was interesting for two reasons: 1) the pupil response was so robust, it was visible in every subject's data. 2) no one seemed to know what the make of it. So unfortunately we had great data, but no 'point' and the project has remained as a interesting conference abstract.

 
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