maandag 18 juni 2012

An Article from PLoS: The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

Jonas Kubilius has sent you an open-access article from PLoS ONE.

The sender added this:

This is a rather crazy paper stating that your fMRI analysis results can depend on your computer and operating system. Not sure what to think about that...

Read the open-access, full-text article here:
http://dx.plos.org/10.1371/journal.pone.0038234

===================================================
The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

Abstract:

FreeSurfer is a popular software package to measure cortical thickness and volume of neuroanatomical structures. However, little if any is known about measurement reliability across various data processing conditions. Using a set of 30 anatomical T1-weighted 3T MRI scans, we investigated the effects of data processing variables such as FreeSurfer version (v4.3.1, v4.5.0, and v5.0.0), workstation (Macintosh and Hewlett-Packard), and Macintosh operating system version (OSX 10.5 and OSX 10.6). Significant differences were revealed between FreeSurfer version v5.0.0 and the two earlier versions. These differences were on average 8.8±6.6% (range 1.3–64.0%) (volume) and 2.8±1.3% (1.1–7.7%) (cortical thickness). About a factor two smaller differences were detected between Macintosh and Hewlett-Packard workstations and between OSX 10.5 and OSX 10.6. The observed differences are similar in magnitude as effect sizes reported in accuracy evaluations and neurodegenerative studies.

The main conclusion is that in the context of an ongoing study, users are discouraged to update to a new major release of either FreeSurfer or operating system or to switch to a different type of workstation without repeating the analysis; results thus give a quantitative support to successive recommendations stated by FreeSurfer developers over the years. Moreover, in view of the large and significant cross-version differences, it is concluded that formal assessment of the accuracy of FreeSurfer is desirable.

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maandag 19 maart 2012

Fwd: Similar spatial patterns of neural coding of category selectivity in FFA and VWFA under different attention conditions



------- Forwarded message -------
From: "ScienceDirect Publication: Neuropsychologia" <>
To:
Cc:
Subject: Similar spatial patterns of neural coding of category selectivity in FFA and VWFA under different attention conditions
Date: Mon, 19 Mar 2012 10:01:34 +0100

Publication year: 2012
Source:Neuropsychologia, Volume 50, Issue 5

Guifang Xu, Yi Jiang, Lifei Ma, Zhi Yang, Xuchu Weng

It has long been debated whether attention alters the categorical selectivity in regions such as the fusiform face area (FFA) and the visual word form area (VWFA). We addressed this issue by examining whether the spatial pattern of neural representations for certain stimulus categories in these regions would change under different attention conditions. Faces, Chinese characters, and textures were presented in a block design fMRI experiment where participants in different runs attended to the stimuli under different conditions of attention. After localizing regions of interest (ROIs) in FFA and VWFA using general linear models, we performed spatial pattern analyses to examine both within- and cross-condition classification in these ROIs. The within-condition results replicated previous findings showing significant classification accuracy reduction when there was less attention compared with more attention. Critically, cross-condition classification in both FFA and VWFA revealed significantly above-chance accuracy for all stimulus categories, suggesting similar spatial neural representations across different attention conditions. Further strengthening this conclusion, when the contrast-to-noise ratio (CNR) of the signals was adjusted to increase signal strength, cross-condition classification accuracy for faces in FFA and for Chinese characters in VWFA improved significantly, even approaching within-condition accuracy. This indicates that attention does not modulate the spatial pattern of neural representations involved in category selectivity, but only changes the signal strength relative to the noise level.




Full article



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maandag 12 maart 2012

Fwd: Computational advances towards linking BOLD and behavior



------- Forwarded message -------
From: "ScienceDirect Publication: Neuropsychologia" <>
To:
Cc:
Subject: Computational advances towards linking BOLD and behavior
Date: Mon, 12 Mar 2012 11:48:19 +0100

Publication year: 2012
Source:Neuropsychologia, Volume 50, Issue 4

John T. Serences, Sameer Saproo

Traditionally, fMRI studies have focused on analyzing the mean response amplitude within a cortical area. However, the mean response is blind to many important patterns of cortical modulation, which severely limits the formulation and evaluation of linking hypotheses between neural activity, BOLD responses, and behavior. More recently, multivariate pattern classification analysis (MVPA) has been applied to fMRI data to evaluate the information content of spatially distributed activation patterns. This approach has been remarkably successful at detecting the presence of specific information in targeted brain regions, and provides an extremely flexible means of extracting that information without a precise generative model for the underlying neural activity. However, this flexibility comes at a cost: since MVPA relies on pooling information across voxels that are selective for many different stimulus attributes, it is difficult to infer how specific sub-sets of tuned neurons are modulated by an experimental manipulation. In contrast, recently developed encoding models can produce more precise estimates of feature-selective tuning functions, and can support the creation of explicit linking hypotheses between neural activity and behavior. Although these encoding models depend on strong – and often untested – assumptions about the response properties of underlying neural generators, they also provide a unique opportunity to evaluate population-level computational theories of perception and cognition that have previously been difficult to assess using either single-unit recording or conventional neuroimaging techniques.




Full article



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woensdag 30 november 2011

Attention Reverses the Effect of Prediction in Silencing Sensory Signals

Abstract

Predictive coding models suggest that predicted sensory signals are attenuated (silencing of prediction error). These models, though influential, are challenged by the fact that prediction sometimes seems to enhance rather than reduce sensory signals, as in the case of attentional cueing experiments. One possible explanation is that in these experiments, prediction (i.e., stimulus probability) is confounded with attention (i.e., task relevance), which is known to boost rather than reduce sensory signal. However, recent theoretical work on predictive coding inspires an alternative hypothesis and suggests that attention and prediction operate synergistically to improve the precision of perceptual inference. This model posits that attention leads to heightened weighting of sensory evidence, thereby reversing the sensory silencing by prediction. Here, we factorially manipulated attention and prediction in a functional magnetic resonance imaging study and distinguished between these 2 hypotheses. Our results support a predictive coding model wherein attention reverses the sensory attenuation of predicted signals.



http://cercor.oxfordjournals.org/content/early/2011/11/01/cercor.bhr310.full.pdf+html




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donderdag 6 oktober 2011

Emergence of Perceptual Gestalts in the Human Visual Cortex: The Case of the...

 
 

Sent to you by Frouke via Google Reader:

 
 

via Psychological Science current issue by Kubilius, J., Wagemans, J., Op de Beeck, H. P. on 10/6/11

Many Gestalt phenomena have been described in terms of perception of a whole being not equal to the sum of its parts. It is unclear how these phenomena emerge in the brain. We used functional MRI to study the neural basis of the behavioral configural-superiority effect (i.e., visual search is more efficient when an odd element is part of a configuration than when it is presented by itself). We found that searching for the odd element in a display of four line segments (parts) was facilitated by adding two additional line segments to each of them (creating whole shapes). Functional MRI–based decoding of neural responses to the position of the odd element revealed a neural configural-superiority effect in shape-selective regions but not in low-level retinotopic areas, where decoding of parts was more pronounced. These results show how at least some Gestalt phenomena in vision emerge only at the higher stages of visual information processing and suggest that feed-forward processing might be sufficient to produce such phenomena.


 
 

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dinsdag 27 september 2011

Constructing scenes from objects in human occipitotemporal cortex

Obviously, a must read!

 
 

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per Nature Neuroscience - Issue - nature.com science feeds autorius Russell A Epstein 11.9.4

Constructing scenes from objects in human occipitotemporal cortex

Nature Neuroscience 14, 1323 (2011). doi:10.1038/nn.2903

Authors: Sean P MacEvoy & Russell A Epstein


 
 

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vrijdag 23 september 2011

Reconstructing Visual Experiences from Brain Activity Evoked by Natural Movies

For those browsing their RSS feeds from home, more information on this story here:

https://sites.google.com/site/gallantlabucb/publications/nishimoto-et-al-2011

 
 

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via Gestalt Revision fMRI by Gestalt Revision on 9/23/11

This is really fun! I encourage everybody to look up their supplementary movie.

 
 

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per CURRENT BIOLOGY 11.9.21

Shinji Nishimoto, An T. Vu, Thomas Naselaris, Yuval Benjamini, Bin Yu, Jack L. Gallant. Quantitative modeling of human brain activity can provide crucial insights about cortical representations [1, 2] and can form the basis for brain decoding devices [3–5]. Recent functional magnetic....

 
 

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Reconstructing Visual Experiences from Brain Activity Evoked by Natural Movies

This is really fun! I encourage everybody to look up their supplementary movie.

 
 

Naudojant „Google Reader" atsiųsta jums nuo Jonas:

 
 

per CURRENT BIOLOGY 11.9.21

Shinji Nishimoto, An T. Vu, Thomas Naselaris, Yuval Benjamini, Bin Yu, Jack L. Gallant. Quantitative modeling of human brain activity can provide crucial insights about cortical representations [1, 2] and can form the basis for brain decoding devices [3–5]. Recent functional magnetic....

 
 

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woensdag 14 september 2011

Neuroimaging reveals how brain uses objects to recognize scenes

 
 

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A new study by psychologists helps to explain how people quickly and accurately recognize complicated scenes such as playgrounds, kitchens and traffic intersections.

 
 

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dinsdag 23 augustus 2011

Associative Learning Increases Trial-by-Trial Similarity of BOLD-MRI Patterns

http://www.jneurosci.org/content/31/33/12021.full.pdf+html

 

Associative Learning Increases Trial-by-Trial Similarity of BOLD-MRI Patterns

 

Rene´e M. Visser,

1,2

H. Steven Scholte,

2,3

and Merel Kindt

1,2

1

Department of Clinical Psychology,

2

Priority Program Brain and Cognition, and

3

Department of Brain and Cognition, University of Amsterdam,

1018 WB Amsterdam, The Netherlands

Associative learning is a dynamic process that allows us to incorporate new knowledge within existing semantic networks. Even after

years, a seemingly stable association can be altered by a single significant experience. Here, we investigate whether the acquisition of new

associations affects the neural representation of stimuli and how the brain categorizes stimuli according to preexisting and emerging

associations. Functional MRI data were collected during a differential fear conditioning procedure and at test (4 –5 weeks later). Two

pictures of faces and two pictures of houses served as stimuli. One of each pair coterminated with a shock in half of the trials (partial

reinforcement). Applying Multivoxel Pattern Analysis (MVPA) in a trial-by-trial manner, we quantified changes in the similarity of

neural representations of stimuli over the course of conditioning. Our findings show an increase in similarity of neural patterns throughout the cortex on consecutive trials of the reinforced stimuli. Furthermore, neural pattern similarity reveals a shift from original categories (faces/houses) toward new categories (reinforced/unreinforced) over the course of conditioning. This effect was differentially

represented in the cortex, with visual areas primarily reflecting similarity of low-level stimulus properties (original categories) and

frontal areas reflecting similarity of stimulus significance (new categories). Effects were not dependent on overall response amplitude

and were still presentduring follow-up. We conclude thattrial-by-trial MVPA is a useful tool for examining how the human brain encodes

relevant associations and forms new associative networks.

 

-----------------------------------------------------------

Lee de-Wit (PhD), Post-Doctoral Researcher

Gestalt ReVision Project, University of Leuven.

https://sites.google.com/site/leehdewit/

http://ppw.kuleuven.be/labexppsy/gestaltrevision/

lee.dewit@psy.kuleuven.be, ++32 16 326 143

-----------------------------------------------------------

 

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donderdag 28 juli 2011

Decoding of coherent but not incoherent motion signals in early dorsal visual cortex

http://www.sciencedirect.com/science/article/pii/S1053811910004052#bb0190

 

NeuroImage
Volume 56, Issue 2, 15 May 2011, Pages 688-698
Multivariate Decoding and Brain Reading

http://www.sciencedirect.com/scidirimg/clear.gifdoi:10.1016/j.neuroimage.2010.04.011 | How to Cite or Link Using DOI

  Permissions & Reprints

 

Decoding of coherent but not incoherent motion signals in early dorsal visual cortex

Sponsored Article

Dietrich Samuel Schwarzkopfa, b, low asterisk, E-mail The Corresponding Author, Philipp Sterzerc, 3 and Geraint Reesa, b, 1, 2

a UCL Institute of Cognitive Neuroscience, 17 Queen Square, London WC1N 3AR, UK

b Wellcome Trust Centre for Neuroimaging at UCL, 12 Queen Square, London WC1N 3BG, UK

c Department of Psychiatry, Charité Campus Mitte, Charitéplatz 1, D-10117 Berlin, Germany


Available online 10 April 2010. 

 

Abstract

When several scattered grating elements are arranged in such a way that their directions of motion are consistent with a common path, observers perceive them as belonging to a globally coherent moving object. Here we investigated how this coherence changes the representation of motion signals in human visual cortex using functional magnetic resonance imaging (fMRI) and multivariate voxel pattern decoding, which have the potential to reveal how well a stimulus is encoded in different contexts. Only during globally coherent motion was it possible to reliably distinguish fMRI signals evoked by different directions of motion in early visual cortex. This effect was specific to the retinotopic representation of the visual field quadrant in V1 traversed by the coherent element path and could not simply be attributed to a general increase in signal strength. Decoding was more reliable for cortical areas corresponding to the lower visual field. Because some previous studies observed poorer speed discrimination when motion was grouped, we also conducted behavioural experiments to investigate this with our stimuli, but did not reveal a consistent relationship between coherence and perceived speed. Taken together, these data show that neuronal populations in early visual cortex represent information that could be used for interpreting motion signals as unified objects.

 

 

 

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dinsdag 26 april 2011

Inter-area correlations in the ventral visual pathway reflect feature integr...

 
 

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via Journal of Vision recent issues door Freeman, J., Donner, T. H., Heeger, D. J. op 26-4-11

During object perception, the brain integrates simple features into representations of complex objects. A perceptual phenomenon known as visual crowding selectively interferes with this process. Here, we use crowding to characterize a neural correlate of feature integration. Cortical activity was measured with functional magnetic resonance imaging, simultaneously in multiple areas of the ventral visual pathway (V1–V4 and the visual word form area, VWFA, which responds preferentially to familiar letters), while human subjects viewed crowded and uncrowded letters. Temporal correlations between cortical areas were lower for crowded letters than for uncrowded letters, especially between V1 and VWFA. These differences in correlation were retinotopically specific, and persisted when attention was diverted from the letters. But correlation differences were not evident when we substituted the letters with grating patches that were not crowded under our stimulus conditions. We conclude that inter-area correlations reflect feature integration and are disrupted by crowding. We propose that crowding may perturb the transformations between neural representations along the ventral pathway that underlie the integration of features into objects.


 
 

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dinsdag 7 december 2010

The surface area of human V1 predicts the subjective experience of object size.

The bigger your V1, the less illusions you see...

 
 

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per pubmed: top authors autorius Schwarzkopf DS, Song C, Rees G 10.12.7

Related Articles

The surface area of human V1 predicts the subjective experience of object size.

Nat Neurosci. 2010 Dec 5;

Authors: Schwarzkopf DS, Song C, Rees G

The surface area of human primary visual cortex (V1) varies substantially between individuals for unknown reasons. We found that this variability was strongly and negatively correlated with the magnitude of two common visual illusions, where two physically identical objects appear different in size as a result of their context. Because such illusions dissociate conscious perception from physical stimulation, our findings indicate that the surface area of V1 predicts variability in conscious experience.

PMID: 21131954 [PubMed - as supplied by publisher]


 
 

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maandag 25 oktober 2010

Cognitive neuroscience 2.0: building a cumulative science of human brain function

 

http://www.cell.com/trends/cognitive-sciences/abstract/S1364-6613(10)00201-9

 

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maandag 11 oktober 2010

Interpreting brain images: reflections on an adolescent field

Book review; the book might be interesting.

 

 

Feed: TRENDS IN COGNITIVE SCIENCES
Posted on: dinsdag 28 september 2010 6:00
Author: TRENDS IN COGNITIVE SCIENCES
Subject: Interpreting brain images: reflections on an adolescent field

 

Nikolaus Kriegeskorte.


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dinsdag 5 oktober 2010

Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures

http://www.nature.com/nprot/journal/v5/n3/full/nprot.2009.226.html

-----------------------------------------------------------------------
Naoki Kogo, PhD
Laboratory of Experimental Psychology
Department of Psychology, University of Leuven, Belgium
-----------------------------------------------------------------------

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Optogenetic fMRI Sheds Light on the Neural Basis of the BOLD Signal

 
 

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via Journal of Neurophysiology current issue by Palmer, H. S. on 10/4/10

Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) is widely used as a measure of neuronal activity, despite an incomplete understanding of the hemodynamic and neural bases for BOLD signals. Recent work by Lee and colleagues investigated whether activating genetically specified neurons elicits BOLD responses. Integrating optogenetic control of specific cells and fMRI showed that stimulating excitatory neurons triggers a positive BOLD signal with conventional kinetics locally and delayed weaker BOLD signals distally.


 
 

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Global and local fMRI signals driven by neurons defined optogenetically by t...

 
 

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via Nature - Issue - nature.com science feeds by Karl Deisseroth on 5/16/10

Global and local fMRI signals driven by neurons defined optogenetically by type and wiring

Nature 465, 788 (2010). doi:10.1038/nature09108

Authors: Jin Hyung Lee, Remy Durand, Viviana Gradinaru, Feng Zhang, Inbal Goshen, Dae-Shik Kim, Lief E. Fenno, Charu Ramakrishnan & Karl Deisseroth

Despite a rapidly-growing scientific and clinical brain imaging literature based on functional magnetic resonance imaging (fMRI) using blood oxygenation level-dependent (BOLD) signals, it remains controversial whether BOLD signals in a particular region can be caused by activation of local excitatory neurons. This difficult question is central to the interpretation and utility of BOLD, with major significance for fMRI studies in basic research and clinical applications. Using a novel integrated technology unifying optogenetic control of inputs with high-field fMRI signal readouts, we show here that specific stimulation of local CaMKIIα-expressing excitatory neurons, either in the neocortex or thalamus, elicits positive BOLD signals at the stimulus location with classical kinetics. We also show that optogenetic fMRI (ofMRI) allows visualization of the causal effects of specific cell types defined not only by genetic identity and cell body location, but also by axonal projection target. Finally, we show that ofMRI within the living and intact mammalian brain reveals BOLD signals in downstream targets distant from the stimulus, indicating that this approach can be used to map the global effects of controlling a local cell population. In this respect, unlike both conventional fMRI studies based on correlations and fMRI with electrical stimulation that will also directly drive afferent and nearby axons, this ofMRI approach provides causal information about the global circuits recruited by defined local neuronal activity patterns. Together these findings provide an empirical foundation for the widely-used fMRI BOLD signal, and the features of ofMRI define a potent tool that may be suitable for functional circuit analysis as well as global phenotyping of dysfunctional circuitry.


 
 

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donderdag 23 september 2010

Modeling and analyzing mechanisms underlying fMRI-based decoding of information conveyed in cortical columns

 

Feed: ScienceDirect Publication: NeuroImage
Posted on: donderdag 23 september 2010 7:04
Author: ScienceDirect Publication: NeuroImage
Subject: Modeling and analyzing mechanisms underlying fMRI-based decoding of information conveyed in cortical columns

 

Publication year: 2010
Source: NeuroImage, In Press, Accepted Manuscript, Available online 22 September 2010
Denis, Chaimow , Essa, Yacoub , Kamil, Ugurbil , Amir, Shmuel
Multivariate machine learning algorithms applied to human functional MRI (fMRI) data can decode information conveyed by cortical columns, despite the voxel-size being large relative to the width of columns. Several mechanisms have been proposed to underlie decoding of stimulus orientation or the stimulated eye. These include: (I) aliasing of high spatial-frequency components, including the main frequency of the columnar organization by the large voxels, (II) contributions from local irregularities in the columnar organization, (III) contributions from large-scale non-columnar organizations (IV), functionally selective veins with biased draining regions, and (V) complex spatio-temporal filtering of neuronal activity by fMRI voxels. Here we...


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woensdag 22 september 2010

Self-organisation in the human visual system–visuo-motor processing with congenitally abnormal V1 input

 

Feed: ScienceDirect Publication: Neuropsychologia
Posted on: woensdag 22 september 2010 6:25
Author: ScienceDirect Publication: Neuropsychologia
Subject: Self-organisation in the human visual system–visuo-motor processing with congenitally abnormal V1 input

 

Publication year: 2010
Source: Neuropsychologia, In Press, Accepted Manuscript, Available online 21 September 2010
Barbara, Wolynski , Martin, Kanowski , Synke, Meltendorf , Wolfgang, Behrens-Baumann , Michael B., Hoffmann
Due to an abnormal projection of the temporal retina the albinotic primary visual cortex receives substantial input from the ipsilateral visual field. To test whether representation abnormalities are also evident in higher tier visual, and in motor and somatosensory cortices, brain activity was measured with fMRI in 14 subjects with albinism performing a visuo-motor task. During central fixation, a blue or red target embedded in a distractor array was presented for 250ms in the left or right visual hemifield. After a delay, the subjects were prompted to indicate with left or right thumb button presses the target presence in the...


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