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8

As a slight modification of your statement: blood flow increases wherever activity in the brain increases. The type of fMRI that uses this principle is blood-oxygenation-level-dependent fMRI or BOLD fMRI. MRI in general detects signals by picking up proton signals from water molecules. This proton signal is basically caused by magnetizing the protons ...


6

I'm only going to attempt to answer a small part of your question: how does glial activation affect the blood oxygen level-dependent (BOLD) response measured by fMRI? Schulz et al. (2012) were able to investigate the role of glial signaling on fMRI activity by simultaneously measuring neuronal responses with invasive optical imaging and fMRI. They found ...


5

Have you tried: connectomeviewer http://www.connectomeviewer.org/viewer brainnetviewer http://www.nitrc.org/projects/bnv/ which is a toolbox for the SPM software package http://www.fil.ion.ucl.ac.uk/spm/ Gephi http://gephi.org/ Trackvis http://trackvis.org/ Also Nico Dosenbach has some amazing picture of brain connectivity in this paper ...


4

This question gets close to something that might alternatively be posted to stats.stackoverflow.com. Personally, I've always felt that application of Null-Hypothesis Significance Testing (NHST) methods to neuroimaging data does a particularly good job of highlighting their scientific deficiencies. Personally, these days I'd use Generalized Additive ...


3

The best way to learn is probably not by reading, but by doing. The SPM website contains a number of useful datasets with tutorials for various tasks. I also find PowerPoint slides from lectures and talks useful. There are a bunch of slides on the SPM website, but you can also find more on Google by limiting your results to type:pptx.


3

Replicating fMRI signal was first used in the Tower of Hanoi task as seen in section 5.8 of "How to Build a Brain": There is strong evidence that dendritic processing, driven by neurotransmitter usage, underwrites the BOLD signal (Logothetis & Wandell, 2004). It is that BOLD signal that is actually measured by MRI machines. Consequently, MRI ...


3

Great question! To start, you are absolutely right-- a 1997 article on fMRI is considered very old as far as the field is concerned. Statistical techniques have improved dramatically since then so, while I haven't read the article in question, it's safe to assume that there are probably lots of things they would do differently if the study was conducted ...


3

Dario Ringach wrote in a letter titled Neuroscience: States of Mind: (inline references removed, see link for references) If the ability to perceive oriented stimuli is found to depend on the cortical state, we can then ask a number of important questions about cortical function. Is the time the cortex spends visiting particular states a function ...


3

The fMRI Data Center (www.fmridc.org) was one such repository. About ten years ago it was a requirement for publication in the Journal of Cognitive Neuroscience that you submit your full fMRI dataset to the fMRIDC. This requirement was only around for a few years, but they ended up having 120+ datasets before the grant funding ran out. The archive is ...


2

Totally out of my league here, but judging from a quick Google search, this seems to be a common problem in FSL. You've said this YouTube video helps, so that's good...but since it uses an applescript, I suppose it requires the Mac OS. You say Freesurfer's mri_convert works in Linux using this code: mri_convert --in_orientation [file's current storage ...


2

Answering to my own question: Avogadro is a molecule editor, but for visualization purposes it does not check the validity of the molecule, thus permitting its usage in the creation of publication-quality 3D ball-and-stick models of any subject matter, such as brain connectivity networks. Avogadro reads several molecule file formats, for example .cml is an ...


2

I'm not an expert in neuroimaging, so I had to search a little bit to learn about how carry-over designs apply to fMRI (I found Aguirre, 2007). Thus, feel free to correct me if there is something specific about this problem domain that influences the correct answer to this question. However, based on general principles of experimental design of repeated ...


2

Ha, I was going to mention the Kok Neuron paper :) The Cerebral Cortex one does not use decoding however. This one may also be of interest to you: Vetter, P., Smith, F. W., & Muckli, L. (2014). Decoding Sound and Imagery Content in Early Visual Cortex. Current Biology, 24(11), 1256-1262. Lars Muckli is in general someone who might have more of the ...


2

I don't know any such group in Italy but there is a group in Liege, Belgium which is called Coma Science Group. It consists of scientists of various disciplines and their main interest is understanding disorders of consciousness. Also their work has a clinical orientation as well. From your description, I think it will be interesting to you. Their website is ...


2

This might be better suited as a comment, but I'm not allowed to post such. I went through the nice list collected by Craig Bennett: nitrc.org: Data has been preprocessed, but there is no complete list of what has been done, and how the data has been collected. Maybe the information is hidden in the previous publications. Anyway, I would not use it for ...


1

They used MRI to compare asymmetry in hemispheric volumes across the groups. Hemispheric volume is not something that is changing over time, and so it doesn't require the use of functional neuroimaging (e.g., fMRI). Instead, if we want to be accurate when measuring volume and making comparisons across groups, we need to have high spatial resolution of the ...



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