Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain

Requiring only minimal assumptions for validity, nonparametric permutation testing provides a flexible and intuitive methodology for the statistical analysis of data from functional neuroimaging experiments, at some computational expense. Introduced into the functional neuroimaging literature by Holmes et al. ([1996]: J Cereb Blood Flow Metab 16:7-22), the permutation approach readily accounts for the multiple comparisons problem implicit in the standard voxel-by-voxel hypothesis testing framework. When the appropriate assumptions hold, the nonparametric permutation approach gives results similar to those obtained from a comparable Statistical Parametric Mapping approach using a general linear model with multiple comparisons corrections derived from random field theory. For analyses with low degrees of freedom, such as single subject PET/SPECT experiments or multi-subject PET/SPECT or fMRI designs assessed for population effects, the nonparametric approach employing a locally pooled (smoothed) variance estimate can outperform the comparable Statistical Parametric Mapping approach. Thus, these nonparametric techniques can be used to verify the validity of less computationally expensive parametric approaches. Although the theory and relative advantages of permutation approaches have been discussed by various authors, there has been no accessible explication of the method, and no freely distributed software implementing it. Consequently, there have been few practical applications of the technique. This article, and the accompanying MATLAB software, attempts to address these issues. The standard nonparametric randomization and permutation testing ideas are developed at an accessible level, using practical examples from functional neuroimaging, and the extensions for multiple comparisons described. Three worked examples from PET and fMRI are presented, with discussion, and comparisons with standard parametric approaches made where appropriate. Practical considerations are given throughout, and relevant statistical concepts are expounded in appendices.

/pdf/nonparametric-permutation-tests-for-functional-neuroimaging-2tnaunteli.pdf

Nonparametric permutation tests for functional neuroimaging: A primer with examples

From the Publisher:
The old opposition of matter versus mind stubbornly persists in the way we study mind and brain. In treating cognition as problem solving, Andy Clark suggests, we may often abstract too far from the very body and world in which our brains evolved to guide us. Whereas the mental has been treated as a realm that is distinct from the body and the world, Clark forcefully attests that a key to understanding brains is to see them as controllers of embodied activity. From this paradigm shift he advances the construction of a cognitive science of the embodied mind.

/pdf/being-there-putting-brain-body-and-world-together-again-31tt4y51ml.pdf

Being There: Putting Brain, Body, and World Together Again

The borders of human visual areas V1, V2, VP, V3, and V4 were precisely and noninvasively determined. Functional magnetic resonance images were recorded during phase-encoded retinal stimulation. This volume data set was then sampled with a cortical surface reconstruction, making it possible to calculate the local visual field sign (mirror image versus non-mirror image representation). This method automatically and objectively outlines area borders because adjacent areas often have the opposite field sign. Cortical magnification factor curves for striate and extrastriate cortical areas were determined, which showed that human visual areas have a greater emphasis on the center-of-gaze than their counterparts in monkeys. Retinotopically organized visual areas in humans extend anteriorly to overlap several areas previously shown to be activated by written words.

https://www.cogsci.ucsd.edu/~sereno/papers/HumanRetin95.pdf

Borders of multiple visual areas in humans revealed by functional magnetic resonance imaging

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its discovery was an unexpected consequence of brain-imaging studies first performed with positron emission tomography in which various novel, attention-demanding, and non-self-referential tasks were compared with quiet repose either with eyes closed or with simple visual fixation. The default mode network consistently decreases its activity when compared with activity during these relaxed nontask states. The discovery of the default mode network reignited a longstanding interest in the significance of the brain's ongoing or intrinsic activity. Presently, studies of the brain's intrinsic activity, popularly referred to as resting-state studies, have come to play a major role in studies of the human brain in health and disease. The brain's default mode network plays a central role in this work.

The Brain's Default Mode Network

When the landmark patient Phineas Gage died in 1861, no autopsy was performed, but his skull was later recovered. The brain lesion that caused the profound personality changes for which his case became famous has been presumed to have involved the left frontal region, but questions have been raised about the involvement of other regions and about the exact placement of the lesion within the vast frontal territory. Measurements from Gage's skull and modern neuroimaging techniques were used to reconstitute the accident and determine the probable location of the lesion. The damage involved both left and right prefrontal cortices in a pattern that, as confirmed by Gage's modern counterparts, causes a defect in rational decision making and the processing of emotion.

http://science.sciencemag.org/content/sci/264/5162/1102.full.pdf

The return of Phineas Gage: clues about the brain from the skull of a famous patient

We describe Chromium, a system for manipulating streams of graphics API commands on clusters of workstations. Chromium's stream filters can be arranged to create sort-first and sort-last parallel graphics architectures that, in many cases, support the same applications while using only commodity graphics accelerators. In addition, these stream filters can be extended programmatically, allowing the user to customize the stream transformations performed by nodes in a cluster. Because our stream processing mechanism is completely general, any cluster-parallel rendering algorithm can be either implemented on top of or embedded in Chromium. In this paper, we give examples of real-world applications that use Chromium to achieve good scalability on clusters of workstations, and describe other potential uses of this stream processing technology. By completely abstracting the underlying graphics architecture, network topology, and API command processing semantics, we allow a variety of applications to run in different environments.

/pdf/chromium-a-stream-processing-framework-for-interactive-1tfd70mlj5.pdf

Chromium: a stream-processing framework for interactive rendering on clusters

Brainvox: An Interactive, Multimodal Visualization and Analysis System for Neuroanatomical Imaging

We describe a multistep technique for three-dimensional reconstruction and analysis of brain lesions in vivo, based on the manipulation of magnetic resonance raw data obtained with a special protocol. The technique permits the direct visual identification of neuroanatomical landmarks in each brain specimen and eliminates the need to rely on averaged templates of human brain sections, which can be a source of lesion localization error. The technique also allows for the bidirectional cross-reference between data points in two-dimensional slices and in volume reconstruction and for the projection of subcortical structures onto the three-dimensional cortical surface. The three-dimensional lesion mapping technique can be applied to research with the lesion method in both human and nonhuman primates, to the planning of neurosurgical lesion approach, and to the teaching of neuroanatomy.

Three-dimensional in vivo mapping of brain lesions in humans.

The evolution of the frontal lobes: a volumetric analysis based on three-dimensional reconstructions of magnetic resonance scans of human and ape brains

R.J. Frank

Papers

The return of Phineas Gage: clues about the brain from the skull of a famous patient

Chromium: a stream-processing framework for interactive rendering on clusters

Brainvox: An Interactive, Multimodal Visualization and Analysis System for Neuroanatomical Imaging

Three-dimensional in vivo mapping of brain lesions in humans.

The evolution of the frontal lobes: a volumetric analysis based on three-dimensional reconstructions of magnetic resonance scans of human and ape brains