Tuesday, March 06, 2007


attention: Reference Scan has moved to shiny new Wordpress-powered digs at http://www.refscan.info so please update your bookmarks!


Thursday, January 20, 2005


I apologize for the lack of posts recently, and want to thank those of you who have emailed me expressing interest in the blog. I am finally writing for my dissertation and so am going to be distracted for a few months yet until everything is finalized. In the meantime, I will set up a Yahoo News RSS feed on the sidebar for MRI-related stories. That will be updated as often as Yahoo refreshes their feed, so it should be fairly current. Please do leave comments to this post on other links related to MRI that you find interesting, as it would be wonderful to get healthy discussion and a bona-fide community coalesce here.

Stay tuned, and speak your mind!

Men and women use different brain areas to achieve similar IQ results

Haier RJ, Jung RE, Yeo RA, Head K, Alkire MT. Structural brain variation and general intelligence. Neuroimage. 2004 Sep;23(1):425-33. PDF/HTML via ScienceDirect

Abstract. Total brain volume accounts for about 16% of the variance in general intelligence scores (IQ), but how volumes of specific regions-of-interest (ROIs) relate to IQ is not known. We used voxel-based morphometry (VBM) in two independent samples to identify substantial gray matter (GM) correlates of IQ. Based on statistical conjunction of both samples (N = 47; P < 0.05 corrected for multiple comparisons), more gray matter is associated with higher IQ in discrete Brodmann areas (BA) including frontal (BA 10, 46, 9), temporal (BA 21, 37, 22, 42), parietal (BA 43 and 3), and occipital (BA 19) lobes and near BA 39 for white matter (WM). These results underscore the distributed neural basis of intelligence and suggest a developmental course for volume–IQ relationships in adulthood. Keywords: IQ; Brain volume; Morphometry

This is an interesting paper in Neuroimage that seeks a structural correlation of white and gray matter with intelligence scores, in male and female subjects. The study was performed by Haier et al at UC-Irvine, and there is a good layman's summary at the UCI website, which makes the point:

The study shows women having more white matter and men more gray matter related to intellectual skill, revealing that no single neuroanatomical structure determines general intelligence and that different types of brain designs are capable of producing equivalent intellectual performance.

“These findings suggest that human evolution has created two different types of brains designed for equally intelligent behavior,” said Richard Haier, professor of psychology in the Department of Pediatrics and longtime human intelligence researcher, who led the study with colleagues at UCI and the University of New Mexico.
In general, men have approximately 6.5 times the amount of gray matter related to general intelligence than women, and women have nearly 10 times the amount of white matter related to intelligence than men. Gray matter represents information processing centers in the brain, and white matter represents the networking of – or connections between – these processing centers.

This, according to Rex Jung, a UNM neuropsychologist and co-author of the study, may help to explain why men tend to excel in tasks requiring more local processing (like mathematics), while women tend to excel at integrating and assimilating information from distributed gray-matter regions in the brain, such as required for language facility. These two very different neurological pathways and activity centers, however, result in equivalent overall performance on broad measures of cognitive ability, such as those found on intelligence tests.

These are fascinating results, especially since by eschewing the fMRI craze they have been able to exclude any number of confounding sources of correlation that might have undermined the results. Note that this is not the first study[1] to investigate how IQ correlates with gray matter volume, but the gender dimorphism really adds a fascinating twist, especially in light of Harvard President Larry Summers' clumsily-expressed but nevertheless frank and thought-provoking thoughts on the topic of female academic achievement. This study demonstrates that men and women are equal but different, which is a common-sense result.

[1] Neuroimage. 2004 Nov;23(3):800-5, Nat Rev Neurosci. 2004 Jun;5(6):471-82.

Wednesday, October 06, 2004

Fictional force

Frank Wilczek, recent Nobel Laureate, has written an intriguing column in Physics Today about the strangeness of the concept of "Force", which unlike momentum or energy does not have an analogue in the more sophisticated models of reality that physicists have developed since Newton:

Newton's second law of motion, F = ma, is the soul of classical mechanics. Like other souls, it is insubstantial. The right−hand side is the product of two terms with profound meanings. Acceleration is a purely kinematical concept, defined in terms of space and time. Mass quite directly reflects basic measurable properties of bodies (weights, recoil velocities). The left−hand side, on the other hand, has no independent meaning. Yet clearly Newton's second law is full of meaning, by the highest standard: It proves itself useful in demanding situations. Splendid, unlikely looking bridges, like the Erasmus Bridge (known as the Swan of Rotterdam), do bear their loads; spacecraft do reach Saturn.

The paradox deepens when we consider force from the perspective of modern physics. In fact, the concept of force is conspicuously absent from our most advanced formulations of the basic laws. It doesn't appear in Schrödinger's equation, or in any reasonable formulation of quantum field theory, or in the foundations of general relativity.

He spends most of his time discussing what hecalls the "culture" of force, but I was especially struck by this comment which is somewhat tangential to his main point:

Nevertheless it survives the competition, and continues to flourish, for one overwhelmingly good reason: It is much easier to work with. We really do not want to be picking our way through a vast Hilbert space, regularizing and renormalizing ultraviolet divergences as we go, then analytically continuing Euclidean Green's functions defined by a limiting procedure, . . . working to discover nuclei that clothe themselves with electrons to make atoms that bind together to make solids, . . . all to describe the collision of two billiard balls. That would be lunacy similar in spirit to, but worse than, trying to do computer graphics from scratch, in machine code, without the benefit of an operating system. The analogy seems apt: Force is a flexible construct in a high−level language, which, by shielding us from irrelevant details, allows us to do elaborate applications relatively painlessly.

What an interesting analogy! I think however that it can be extended beond the concept of force - to classical vs quantum mechanics as a whole. Classical mechanics itself as a "high-level" language, built upon the "assembly language" foundation of quantum. It occurs to me that much of the elegance of MR physics can be aesthetically understood better in that context.

tortured physics analogies

More broadly, Doerr said he thought of the next phases of Internet development in terms of the scientific theory known as string theory, which posits that there are seven parallel universes. The "near" Web represents the PC; the "far" Web stands for television; the "here" Web represents mobile devices; the "business to business" Web for XML, RSS (Really Simple Syndication) feeds and other backend technologies; and the "weird" Web is for 3D experiences or virtual worlds that could be developed. Doerr said he had yet to come up with the seventh.


Saturday, September 04, 2004

History of MRI website from NAS

There's an excellent, in-depth reference article on the National Academy of Sciences's website about the historical development of MRI. It's grouped into the following sections, each of which are multiple pages:
  1. Summary
  2. Signals from Spinning Nuclei
  3. The Experiments of I. I. Rabi
  4. A Different Kind of Resonance
  5. Listening for Echoes
  6. The Science of Imaging
  7. From Structure to Function
  8. Credits

I think the in-depth focus on Isidor Rabi's work is appropriate. The site frames the history as a march towards functional imaging, but is quite comprehensive with numerous illustrations and even a nifty Timeline feature. Well worth bookmarking, especially if you're a grad student writing your Background section of your dissertation :)

UPDATE: This condensed History of MRI page is also very useful.

Saturday, July 10, 2004


Dr. Peter Kingsley of the North Shore University Hospital in Manhasset, NY was kind enough to point out a small typo in Table 2 of our published manuscript, "Analytical error propagation in diffusion anisotropy calculations" (JMRI 2004; 19:489-498). The corrected Table is reproduced below, with the theta and phi symbols correctly placed.

We also are making our gradient schemes used in that manuscript, in directional cosine format, available here for download (ZIP, 3KB).

We apologise to anyone inconvenienced by the error and are happy to make further information available upon request.

Wednesday, June 30, 2004

Perl script for generating diffusion directions

I am putting into the public domain this Perl script for generating the directional cosines for an arbitrary number of diffusion directions, using a solid-angle tiling approach. The schemes generated with this code were used for the Poonawalla scheme N = 27 and N = 55 in [1] (that reference also compares the conditional number to other schemes such as icosahedral in Table 3).

Note that the code does not perform very well for N less than about 20. This is because the algorithm attempts to subdivide the sphere with circular tiles, which was a crude approximation. The intended use of this code is solely to provide a quick-n-dirty way to generate a usable diffusion scheme, with no claim that it's necessarily the best possible scheme available. But it's simplicity means that it can be adapted for real-time generation of a DTI protocol with much less computational overhead than an electrostatic repulsion model, and you can use any value of N you desire (unlike icosahedral schemes which are limited to specific N values). Please do contact me if you use this code or have suggestions for improvement (patches welcome).


[1] Poonawalla AH, Zhou XJ. Analytical error propagation in diffusion anisotropy calculations. J Magn Reson Imaging 2004;19(4):489-498.

Monday, June 28, 2004

Deus ex fMRI

It's often tempting for scientists to lapse into condescension towards the media portrayal of technology, an attitude which is counterproductive in general, because a partnership with the media is essential for fostering enthusiasm for Science (especially among the young).

Unfortunately, everything reported by the media goes through at least one Sensationalizing filter, which usually is a source of extreme frustration for scientists trying to ensure that their work is accurately described. There is no topic for which this is more true than fMRI research. Quoth Newsweek, in an article disconcertingly titled, "Mind Reading" - which tries to understand the thought process of students playing a variant of the Prisoner's Dilemma via the BOLD effect:

The fMRI machine shows how all this works inside the brain. A low offer stimulates activity in the brain's insular cortex, a relatively primitive region associated with negative emotions including anger and disgust. This appears to compete with the more highly evolved prefrontal cortex, the locus of the rational impulse to take the dollar and go buy a soda with it. The more activity in the insular cortex, the more likely subjects were to reject the offer. This is a big step toward being able to see on a screen what people actually want, rather than what they say in focus groups or interviews. Would brain-scan-assisted matchmaking or employee headhunting be more efficient than the way these have been carried out until now? Or would the fMRI merely ratify the judgments of intuition? Psychologists can hardly wait to find out.

And for their part, economists can hardly contain their glee at the research horizons this opens up. "Imagine if you could go on the floor of the stock exchange and see what was going on in traders' brains," says Camerer. "We kept hearing during the bubble that people were behaving as if they were in a delusional state. Well, were they or weren't they?" People don't save enough for their retirements because of a phenomenon known as forward discounting: they value money more in the here and now than 20 years down the road. If we could understand how this process works in the brain, says Paul Glimcher, a leading neuroscientist at New York University, we would have a head start on figuring out how to overcome it.

The emphasis on economists' (and later, marketers') glee is perhaps telling. To be fair, the article does briefly mention some of the physiological limitations of the fMRI signal, but that doesn't stop further downstream assertions such as:

The same tools that can answer deep questions about primate behavior can also be used to get people to sign up for more cell-phone minutes than there actually are in a month. A handful of researchers in the United States and Europe are already using fMRIs to test how product brands are represented in the brain.

Re-reading what I've written so far, I guess I haven't actually debunked the claims so much as repeat them with a sneer. The main rebuttal is that the physiological delay between the stimulus and the response - averaged over the millions of neurons in the large voxels of interest - is indeed correlated with the underlying thought processes, but it's exceedingly unlikely that any causal relationship can be inferred. You might as well try to understand the mechanics of an athlete's muscle fiber by monitoring their heart rate. But a more thorough discussion is probably better left to the comment section.

Thursday, June 24, 2004

MATLAB code for MRI pulse sequence design

There are some good resources for drawing MRI pulse sequence diagrams in MATLAB available online. One example is pulse.m by T.S. Mahesh, a PhD student in Bangalore. Dr. Mahesh's webpage has moved here, where I presume development of the pulse.m library will continue.

Another excellent resource is the MR Pulse Sequence Diagram Toolbox, originally written by Craig Jones of the University of British Columbia, but no longer available from the original site. I have currently mirrored the MRPSD toolbox here, (mrpsd.zip, 19.1 KB). Since MRPSD was released under the GNU Public License, it can be freely modified, and I intend to update the code with any changes I make at this location. A link to the most recent code is on the blog sidebar, and if any readers have patches to submit, please contact me.

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