18 August 2011

Help, my brain won't normalise!



If you want to make strong, causal inferences about the brain networks supporting a cognitive function, you will probably need to recruit patients with brain lesions. Although fMRI indicates the networks correlated with a particular cognitive factor, fMRI in healthy controls cannot identify the regions that are essential. In contrast, if damage to a region impairs performance, this suggests a direct causal link between this region and cognition, and implies that the region is critical for preserved performance.

Nothing in life is easy, though, and analysing data from patients has its specific challenges. Patients are hard to recruit, and the size and location of their damage is unlikely to match conveniently to the brain areas you study. Once you have the data you need, your troubles are not over: this article deals with the challenge of normalising brain images that include large lesions.

Spatial normalisation is essential for group analysis of brain images. To detect effects in a given region, that region must be in the same place in every individual. In SPM, normalisation works by fitting each image to a template, first using a rough 12- parameter affine transformation (translation, rotation, stretching and skewing in three dimensions) and then using a more detailed non-linear warp (Friston et al. 2007). Warping applies local stretching and shrinking that minimizes the differences between the image and the template. This is great for healthy controls, but when the warping algorithm encounters a large, dark area in the brain it may try to shrink this area to make the image look "normal". Three main strategies have been proposed to deal with this:

Cost function masking
  • Define a mask that covers voxels with damage
  • Carry out warping ignoring voxels in the mask
  • Warp calculated on intact voxels is extrapolated over the masked region
  • Brett et al. (2001)

Unified normalisation
  • Unified normalisation includes a segmentation step
  • Warping is based on the segmented image: only considers tissue of interest
  • This may effectively remove the lesion and make cost function masking redundant
  • Ashburner & Friston (2005)

Warping regularisation
  • Stricter regularisation penalises unlikely warps
  • Makes shrinking of the lesion less likely

Crinion et al. (2007) made a rigorous comparison of unified and standard normalisation, at several levels of warping regulrisation, with or without cost function masking. Unified normalisation performed better than standard overall, reducing the variability in anatomic positioning and slightly improving fMRI results in a group analysis. Within unified normalisation, medium regularisation performed better than either low or high. Cost function masking had an effect only when regularisation was low, suggesting that medium or high regularisation is sufficient to prevent inappropriate warping of the image around the lesion.

The figure below shows images normalised with low (left), medium (middle) and high (right) warping regularisation. Shrinking of the lesion is obvious in low regulrisation.


Crinion et al. focussed on fMRI results as their end point, but warping may also influence VBM using structural images. Stricter warping regularisation may go too far and prevent fit of normal anatomic variations to the template. The figure below shows unified normalisation with strict (left) and medium (right) warping regularisation. The images were skull-stripped with the canonical SPM brain mask as part of preprocessing for VBM. This makes it obvious that strict regularisation prevented a good fit, such the dura was included in the skull-stripped image. [Images modified with photoshop to reduce identifiability].





StrictMedium

Unlike fMRI data, where there is no signal of interest arising from the dura, VBM is intensity-based, and inclusion of dura may substantially alter results. The take-home message here is that you should check the normalisation of each individual image carefully, and consider the suitability of the normalisation method for the type of analysis to be run.

References

Friston KJ, Ashburner JT, Kiebel SJ, Nichols TE, Penny WD (2007) Statistical Parametric Mapping, First Edition. London, UK: Academic Press.
See also: chapter 3 in Human Brain Function, available online http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/

Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial normalization of brain images with focal lesions using cost function masking. Neuroimage 14:486-500.

Ashburner J, Friston KJ (2005) Unified segmentation. Neuroimage 26:839-851.

Crinion J, Ashbumer J, Leff A, Brett M, Price C, Friston K (2007) Spatial normalization of lesioned brains: Performance evaluation and impact on fMRI analyses. Neuroimage 37:866-875.

10 August 2011

Perception and semantics in the ventral stream

One of the goals of cognitive neuroscience is to understand how we process visual objects, and what functional contributions different neural regions make. Our ability to perceive and interact with the world critically relies on the ventral processing stream through occipital and temporal cortices with increasingly anterior portions of the ventral stream responding to increasingly complex stimuli (Taylor, Moss & Tyler, 2007; Felleman & Van Essen, 1991; Tanaka, 1996; Tsunoda et al., 2001). As such, there is a relatively detailed account of how we process objects in a visual sense. However, an aspect of object recognition that is largely avoided concerns what an object means - it’s associated semantic knowledge. Instead, the dominant research strategy is to either focus on object recognition as a purely visual phenomenon, or study semantics without recourse to visual effects.

Recognising what a visual object is not only requires that objects are processed visually, but also that the semantic knowledge associated with the object is evoked. As such, a comprehensive account of how we recognise what an object is requires bringing together theories of visual object recognition, and cognitive models of semantic knowledge within the same neurobiological framework. This is the approach we’ve been developing (see Taylor, Moss & Tyler, 2007 for review) - understanding not only the cognitive contributions of different brain regions, but also how meaning emerges across time (e.g. Clarke, Taylor & Tyler, 2011). Uncovering how we understand what we see requires the development of a comprehensive systems-level account of how we get from perceiving an object, to understanding what it is, and requires the synthesis of cognitive theories and neurobiological models - a fundamental component of cognitive neuroscience.

Clarke, A., Taylor, K.I., & Tyler, L.K. (2011). The evolution of meaning: Spatiotemporal dynamics of visual object recognition Journal of Cognitive Neuroscience, 23(8), 1887-1899.

Felleman, D. J., & Van Essen, D. C. (1991). Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex, 1, 1-47.

Tanaka, K. (1996). Inferotemporal cortex and object vision. Annual Review of Neuroscience, 19, 109-140.

Taylor, K. I., Moss, H. E., & Tyler, L. K. (2007). The conceptual structure account: a cognitive model of semantic memory and its neural instantiation. In J. Hart & M. Kraut (Eds.), The neural basis of semantic memory (pp. 265-301). Cambridge: Cambridge University Press.

Tsunoda, K., Yamane, Y., Nishizaki, M., & Tanifuji, M. (2001). Complex objects are represented in macaque inferotemporal cortex by the combination of feature columns. Nature Neuroscience, 4(8), 832-838.

22 June 2011

Direct Electrical Stimulation: Insight into brain networks

I have just been going through a thought provoking new article by Hughes Duffau (2011), and thought I would provide a brief synopsis of the methods, and highlight a result or two. For those of you who are not very familiar with Direct Electrical Stimulation (DES) work, this would be one of the better places to start, as it is very well written and the reference section covers nearly the entire literature.

The first strength of the paper lies in the methods. Whereas the vast majority of human neuroimaging (MRI, EEG, MEG) attempts to measure cortical activity through the scalp, skull, and meninges, DES goes straight to the source: In patients undergoing brain surgery (awake patients to be specific), bipolar electrode tips deliver biphasic current pulses to the cortex and white matter of the human brain. While the current is being delivered, a patient’s performance on some task is being monitored. When the patient’s performance changes due to the stimulation, you have successfully mapped an “eloquent region.” In other words, that region’s neuronal activity plays a direct role in producing that behaviour.

Dr. Duffau's results using DES support a view of the brain that is very dynamic, and do not adhere to the localization hypothesis. To put it another way, complex human behaviours such as language rely on many different brain regions operating in concert. If one of the regions is damaged, it is possible to re-organize the circuit and preserve the function (as long as the white matter connections are left intact). Bear in mind that this is in relation to so-called frontal/executive functions (cognitive processing, language, emotion, etc), and basic sensory systems might operate far differently (not surprisingly, Dr. Duffau has published on this as well).

Below are a few references... I am including two other intriguing articles for those who want to know more about DES, and how the brain might be wired. As always, email me with any questions or just follow up with a comment.

Duffau H (2011) The “frontal syndrome” revisited: Lessons from electrostimulation mapping studies. Cortex (In Press).

Mandonnet E, Winler PA, Duffau H (2010) Direct electrical stimulation as an input gate into brain functional networks: principles, advantages, and limitations. Acta Neurochirurgica 152: 185-193.

Mandonnet E, Jbabdi S, Taillandier L, Galanaud D, Benali H, Capelle L, Duffau H (2006) Preoperative estimation of residual volume for WHO grade II glioma resected with intraoperative functional mapping. Neuro-Oncology 9: 63-69.

21 June 2011

DTI preprocessing in FSL: B-vector correction

Using FSL to pre-process DTI data is easy to do, and the use of a standard FMRIB pipeline is ubiquitous in the literature. An ongoing concern with this common pre-processing pipeline is how to appropriately deal with eddy currents. FSL uses a 12 degree of freedom affine registration as a method of eddy current correction. By definition, therefore, it corrects for both eddy currents AND gross subject motion. So far this seems great... however...

It is really important to alter your b-vector file based on subject motion (Leemans and Jones 2009), but one should NEVER correct b-vectors based on eddy currents, since these vary across the brain (randomly) depending on a variety of factors. This can have profound effects on not only tractography, but also general diffusion modelling (DTIfit). Current wisdom on the FSL forum suggests that using the downloadable script “rotbvecs” will solve your b-vector correction issue. The problem is that this will correct for both subject motion AND eddy currents.

Here is a simple solution that will allow you to keep using FSL for preprocessing, and keep you up to date on appropriate b-vector corrections:

1) Create a new eddy_correct script that only uses 6-degrees of freedom, and call it eddy_correct_6dof. To do this, just add “-dof 6” to the following line of code:

${FSLDIR}/bin/flirt –in $i –ref ${output}_ref –nosearch –o $i –paddingsize 1

Then run the rotbvecs script as normal (this changes the bvecs file to reflect subject motion).

If you still want to correct for eddy_currents, simply run the regular eddy_correct script, and don’t touch the b-vector file. This might seem like a time consuming extra step, but probabilistic tractography is incredibly sensitive to the initial quality of the data. If you are looking for more detailed instructions, just send me a quick email (look to http://csl.psychol.cam.ac.uk/people/) for my contact info.

Of course ... one can also simply choose not to use FSL to pre-process the data... some great alternatives are emerging.

29 May 2011

Variability and noise in the ageing brain

The vast majority of research reporting age-related changes to neural (e.g. BOLD activity, spike frequencies), behavioural (e.g. reaction times, error rates), or other biological variables is concerned with changes in measures of central tendency (e.g. means), that may change monotonically or nonlinearly with age. Changes to other statistical properties of these variables may also be relevant, however. Variability and/or (when definable) noise are two such properties, and whilst the study of these in the context of ageing is not new, recent findings have some interesting, slightly counterintuitive theoretical implications for how we understand the ageing process.


There are two main strands to this work that comes together nicely - one from cognitive psychology and cognitive neuroimaging (e.g. Garrett, McDonald, Grady), and the other from theoretical and computational neuroscience (e.g. Jirsa, Deco, Ghosh). Randy McIntosh seems to be the link between the two and his 201X review article ties up the two nicely.


The argument goes something like this:


Intra-individual neural variability increases with maturation and declines with senescence, and from a cognitive health point of view the decline is a 'bad' thing...


(Interjection: this is the counterintuitive part, since from both a cognitive and an engineering perspective we normally associate variability with imprecision, inaccuracy, and general lack of system 'integrity'. This leads to an important point:
exactly what variables and what kind of variability we're talking about here is an extremely important detail. More on this below.)


...Both the maturation and senescence patterns are interpreted in terms of there being an "optimal state characterized by a greater ability to transition between brain states and by increased dynamic range", whereas "older, slower, more behaviourally inconsistent participants lack a critical amount of brain variability for optimal neural function" (Garrett et al. 2011). The idea of there being an optimal level of variability/noise (possibly a stochastic resonance effect) has been developed by some of the contributing authors (McIntosh, Jirsa) in a number of simulation studies, where the brain is modelled as a network of coupled oscillators/dynamical systems that display neurophysiologically plausible behaviours such as intermittent synchrony. Their key soundbyte message is that possessing a small amount of endogeneously generated noise facilitates 'exploration of the brain's dynamic repertoire' - i.e. the space of possible brain states (see McIntosh et al. (2010) for a review that brings together the ageing data and the dynamical systems ideas most comprehensively). Other explanations offered by Garrett et al. (2011) for the reduced variability in old age are weakened functional connectivity (c.f. Fox et al. 2006; Nir et al. 2008), poorer neuronal signal detection (Li et al. 2006), or reduced dynamic range (Shew et al. 2009), and some vague comments linking it to 'Bayesian Brain' theories.


I think this is a fascinating and exciting hypothesis and am keen to see how it develops over the next few years. Here's my thoughts:




Comments + criticisms:




1. The list of empirical studies showing decreased variability/noise with (old) age is still quite low: 
  • Garrett et al. (2010a):  examined effects of age on both mean- and standard deviation- (SD) based patterns of Blood Oxygenation Level Dependent (BOLD) signal in a simple visual fixation task. Although both the mean- and SD-based patterns were significantly predictive of age, the significance of the SD-based pattern was more than five times that of the mean-based pattern. Moreover, the brain regions comprising the multivariate spatial patterns identified by the SD-based and mean-based versions of their technique were non-overlapping - indicating that age-related changes in BOLD signal variability (measured here through standard deviation) constitute a distinct neural signature from changes in mean BOLD signal.
  • Garrett et al. (2011): Similar to Garrett et al. (2010a), but different task and subjects (?)
  • Park et al. (2010): Different group, different analysis methods: "Neural specificity was estimated based on how accurately multivariate pattern analysis identified neural activation patterns associated with specific experimental conditions.". Conclusion = loss of neural specificity (which they interpret as de-differentiation) contributes to reduced fluid processing ability in old age. 
  • (for maturation: McIntosh et al (2008): found that intra-trial EEG signal variability decreased between the ages of 8 and 25 years. The level of variability was highly correlated with performance on a face memory task, and so the authors conclude that the move towards greater variability in brain activity during development improves cognitive flexibility and capacity)
  • (in cardiac electrophysiology: Costa et al. (2005) develop a multi-scale entropy measure (which I believe is also used by Vakorin & McIntosh on EEG data) and apply it to cardiogram data, concluding that "The method consistently indicates a loss of complexity with aging, with an erratic cardiac arrhythmia satrial fibrillationd, and with a life-threatening syndrome scongestive heart failured....The results support a general “complexity-loss” theory of aging and disease")
  • (in human motor control, Costa et al. (2007) apply the same measure to demonstrate that application of subsensory noise to the feet improves postural stability and multiscale complexity of sway fluctuations in healthy elderly subjects) 

2. Noise

One of the seminal recent works discussing variability and noise in the nervous system is Faisal et al. (2008), who define 'variability' as simply


“…changes in some measurable quantity, such as spike timing, or movement duration”. 


They also offer the following definition of noise (the subject of their review), following the Oxford English Dictionary:


 “…random or irregular fluctuations or disturbances which are not part of a signal […] or which interfere with or obscure a signal or more generally any distortions or additions which interfere with the transfer of information”.


Faisal et al. note that the term variability, unlike the term noise, is


a) agnostic to the source of the variability (random / deterministic), and


b) carries no implications of being either beneficial or detrimental.




We can add to these a further point, namely that 'variability', unlike 'noise'


c) does not necessitate a signal processing or information-theoretic interpretation of the phenomenon under investigation,


which is clearly not the case for the OED definition given above.


This final point reflects limitations of both the experimentalist and the theoretician, as it is simply not possible at our present level of understanding and technical finesse to define concretely the signals that a given pattern of neural activity might constitute or represent, beyond certain early sensory systems. And since you can only define 'noise' when you can define a 'signal', the fact that some of the papers discussed above use 'variability' and 'noise' are used interchangeably, is a bit sloppy.


The authors are of course aware of this, e.g. McIntosh et al. (2010) say


"An important clarification here is that while these three measures are sensitive to different aspects of  the brain signal, at present we take the liberty of considering them all as measures of brain noise. We acknowledge that this is not ideal, as noise has different implications at different levels of the system."

I think they sometimes they go for 'noise' rather than 'variability' because it sounds jazzier.

Another reason not to use the term noise is because of potential confusion with 'noisy brain' theories of sensory ageing, which go back several decades (e.g. Slathouse & Lichty 1985; Gregory?). Moreover, in electrophysiology studies of early sensory systems where signals can be straightforwardly defined, neurons older animals (monkeys) show increased spontaneous action potential firing rates, decreased stimulus selectivity, and lower signal-to-noise ratios (Schmolensky et al. 2000, Hua et al. 2006,Yu et al. 2006, Yang et al. 2009, Liang et al. 2010). Dopamine may also play a signal-enhancement role in cortical function, its steady decrease with age thus potentially also contributing to increased neural noise (e.g. Li et al.2001).




3. Relation to de-differentiation?


Park et al.  (2010) consider age-related increases in variability of multivariate spatial BOLD activity patterns as an index of 'decreased neural specificity', i.e. de-differentiation. Is this inconsistent with Garrett et al. 's ideas? This would seem to be the case for any spatial (rather than temporal) measure of variability.




References:


Costa et al. (2002a). Multiscale  entropy analysis of complex physiologic time series. Phys. Rev. Lett., 89: 068102

Costa et al. (2005). Multiscale entropy analysis of biological signals. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 71: 021906, 2005.

Deco et al. (2009). Key role of coupling, delay, and noise in resting brain fluctuations. PNAS 106, 10302-10307

Faisal et al. (2008). Noise in the nervous system. Nat. Rev. Neurosci 9, 292-303

Garrett et al. (2010). Blood Oxygen Level-Dependent Signal Variability Is More than Just Noise. J. Neurosci. 30, 4914-4921.

Ghosh et al. (2008). Noise during Rest Enables the Exploration of the Brainʼs Dynamic Repertoire. PLoS Comp Biol 4(10), 12.

Grady et al. (2010). A Multivariate Analysis of Age-Related Differences in Default Mode and Task-Positive Networks across Multiple Cognitive Domains. Cereb. Cortex 20, 1432-144.

Li et al. (2006). A neurocomputational model of stochastic resonance and aging. Neurocomputing, 69(13-15), 1553-1560.

Liang et al. (2010). Aging affects the direction selectivity of MT cells in rhesus monkeys. Neurobiology of Aging 31, 863-873

MacDonald et al. (2003). Performance variability is related to change in cognition: Evidence from the Victoria Longitudinal Study. Psychology and Aging 18, 510-523.

McIntosh et al. (2008). Increased brain signal variability accompanies lower behavioral variability in development.  PLoS Comput. Biol., 4: e1000106.

McIntosh et al. (2010). The development of a noisy brain. Archives Italiennes De Biologie,148(3), 323-337.

Park et al. (2010). Neural specificity predicts fluid processing ability in older adults. Journal of Neuroscience, 30(27), 9253-9259.

Salthouse & & Lichty (1985). Tests of the neural noise hypothesis of age-related cognitive change. J Gerontol 40, 443-450.
  
Schmolesky et al. (2000). Degradation of stimulus selectivity of visual cortical cells in senescent rhesus monkeys. Nature Neuroscience 3, 384-390.

Yang et al. (2009). Aging Affects the Neural Representation of Speed in Macaque Area MT. Cereb. Cortex 19, 1957-1967

Yu et al. (2006). Functional degradation of extrastriate visual cortex in senescent rhesus monkeys. Neuroscience 140, 1023-1029.




See also:

Anstey et al. (1999). Sensorimotor Variables and Forced Expiratory Volume as Correlates of Speed, Accuracy, and Variability in Reaction Time Performance in Late Adulthood. Aging, Neuropsychology, and Cognition 6, 84.

Hultsch  & MacDonald (2004). Intraindividual variability in performance as a theoretical window onto cognitive aging. New Frontiers in Cognitive Aging 65–88

Nesselroade, & Salthouse (2004). Methodological and Theoretical Implications of Intraindividual Variability in Perceptual-Motor Performance. Journals of Gerontology - Series B Psychological Sciences and Social Sciences 59, (2004).

Rabbitt et al. (2001). There are stable individual differences in performance variability, both from moment to moment and from day to day. The Quarterly Journal of Experimental Psychology A 54, 981-1003 (2001).

Suckling et al. (2008). Endogenous multifractal brain dynamics are modulated by age, cholinergic blockade and cognitive performance. Journal of Neuroscience Methods 174, 292-300.


Vakorin et al. (2011). Variability of brain signals processed locally transforms into higher connectivity with brain development. J Neurosci. 31(17): 6405-13.



Welford, A.T (1984). Between bodily changes and performance: some possible reasons for slowing with age. Exp Aging Res 10, 73-88.

Welford, A.T. (1981). Signal, Noise, Performance, and Age. Human Factors: The Journal of the Human Factors and Ergonomics Society 23, 97-109


JG





Introducing 'Wired Minds'....

Welcome, welcome, one and all - we are delighted to announce that 'Wired Minds', the official CSLB lab blog, is now open for business.

As a group our research spans a wide range of topics - including computational linguistics, psycholinguistics, the neural bases of language comprehension, language production, visual object processing, and how these are affected (or not) in healthy ageing and brain damage such as stroke.

Whilst some bias towards these topics is inevitable, the intention with 'Wired Minds' is to provide a general forum for discussion on topics in the field of cognitive neuroscience (broadly conceived). The intention is not so much an exercise in 'science communication' (plenty of these already) as a snapshot of 'science in practice' - with a mix of theoretical, technical, and practical issues.

We warmly welcome contributions from outside the CSLB - the more Wired Minds the better.

Enjoy!

JG