Thursday, 7 October 2010

Science. Doncha love it?

And envy it too...?

I just love this report from California:

Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon:
An argument for multiple comparisons correction
Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford

INTRODUCTION
With the extreme dimensionality of functional neuroimaging data comes extreme risk for false positives. Across the 130,000 voxels in a typical fMRI volume the probability of a false positive is almost certain. Correction for multiple comparisons should be completed with these datasets, but is often ignored by investigators. To illustrate the magnitude of the problem we carried out a real experiment that demonstrates the danger of not correcting for chance properly.
METHODS
Subject. One mature Atlantic Salmon (Salmo salar) participated in the fMRI study. The salmon was approximately 18 inches long, weighed 3.8 lbs, and was not alive at the time of scanning.
Task. The task administered to the salmon involved completing an open-ended mentalizing task. The salmon was shown a series of photographs depicting human individuals in social situations with a specified emotional valence. The salmon was asked to determine what emotion the individual in the photo must have been experiencing.
Design. Stimuli were presented in a block design with each photo presented for 10 seconds followed by 12 seconds of rest. A total of 15 photos were displayed. Total scan time was 5.5 minutes.
Preprocessing. Image processing was completed using SPM2. Preprocessing steps for the functional imaging data included a 6-parameter rigid-body affine realignment of the fMRI timeseries, coregistration of the data to a T1-weighted anatomical image, and 8 mm full-width at half-maximum (FWHM) Gaussian smoothing.
Analysis. Voxelwise statistics on the salmon data were calculated through an ordinary least-squares estimation of the general linear model (GLM). Predictors of the hemodynamic response were modeled by a boxcar function convolved with a canonical hemodynamic response. A temporal high pass filter of 128 seconds was include to account for low frequency drift. No autocorrelation correction was applied.
Voxel Selection. Two methods were used for the correction of multiple comparisons in the fMRI results. The first method controlled the overall false discovery rate (FDR) and was based on a method defined by Benjamini and Hochberg (1995). The second method controlled the overall familywise error rate (FWER) through the use of Gaussian random field theory. This was done using algorithms originally devised by Friston et al. (1994).
DISCUSSION
Can we conclude from this data that the salmon is engaging in the perspective-taking task? Certainly not. What we can determine is that random noise in the EPI timeseries may yield spurious results if multiple comparisons are not controlled for. Adaptive methods for controlling the FDR and FWER
are excellent options and are widely available in all major fMRI analysis packages. We argue that relying on standard statistical thresholds (p < 0.001) and low minimum cluster sizes (k > 8) is an ineffective control for multiple comparisons. We further argue that the vast majority of fMRI studies should be utilizing multiple comparisons correction as standard practice in the computation of their statistics.
REFERENCES
Benjamini Y., Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B, 57:289-300.

Friston, K. J., Worsley, KJ, Frackowiak, R.S. J., Mazziotta, J. C., Evans, A. C. (1994). Assessing the
significance of focal activations using their spatial extent. Human Brain Mapping, vol. 1, pp. 214-220.

The above was taken from a poster presentation to the conference Human Brain Mapping, San Francisco, 2009:


I love the story behind it:


And I love the Comments to this, and the links to further comment and discussion that many of them carry. You could go on tracking this out into the Internet into some infinite cyber-regress for hours...

I do like this sort of science. I admire and envy the people in it, and the way in which they talk about it. Such a long way removed from what one has come to expect nearer home!

I came across this dead salmon business by chance, while checking up further on 'blobology', Cordelia Fine's term for the scientifically sloppy over-interpretation of brain scans to prove whatever one wants them to prove (usually something sad, reactionary and deteministic). I had picked up the notion of blobology from a recent blog posting by Susie Mallett:


Thank you, Susie, for introducing Conductive Education to a useful critical concept. I am sure that at the two forthcoming CE congresses, in Würtzburg and Hong Kong, there will be blobologues aplenty to exercise it upon.

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