Education, tips and tricks to help you conduct better fMRI experiments. Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!
I've been banging the drum on systemic LFOs for some time. Here's another example of how not properly thinking through the physiology of the entire human can produce misleading changes in so-called FC in the fMRI data. That said, I don't think Blaise has the full story here, either. For one thing, the big dips in his Fig 1b suggest that something is being partially offset with the on-resonance adjustment that is conducted automatically at the start of each EPI time series, so I have a residual concern that there are magnetic susceptibility effects contributing here somewhere. (Perhaps the magnetic susceptibility effects are what's left to drift higher after RIPTiDe correction, as in Fig 6b, for example.) The point is that not having independent measures of things like arousal, or proper models of physiologic noise components like sLFOs, or a full understanding of what's happening in the scanner hardware (including head support) during the experiment can lead to an assumption that things are neural when there are better explanations available.
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Link added on 6/23/2024: Blaise Frederick discussing systemic LFOs on "Coffee Break!"
The action potential from one neuron may or may not trigger further action potentials in neurons it connects to via synapses. A typical neuron with its single axon may make thousands of synapses to the dendrites of these "downstream" neurons. The locations of the synapses matter, in the sense that position relative to the downstream neuron's cell body provides a sort of weighted importance to any one synapse, as does the type of synapse. For fMRI we don't need to get too deep into the details of these connections, but we do need a basic understanding of the differences between excitatory and inhibitory connections. For the most part, whether a connection is excitatory or inhibitory is determined by the type of neurotransmitter released at the synapse.
First, let's get an overview of types of synapse and neurotransmitter, and the difference between excitatory and inhibitory neurotransmission:
Next, a little more detail and some context:
In case it wasn't already clear, here's a nice explanation linking the pre-synaptic neuron's electrical potential to neurotransmitter release at the synapse:
Categorizing any one neurotransmitter as excitatory or inhibitory is a reflection of its usual effect on the electrochemical potential in post-synaptic neurons. The actual effect on any one post-synaptic neuron - whether that neuron is rendered closer to or farther away from its threshold voltage - can depend on the location of the synapse as well as the neurotransmitter(s) released in the synaptic cleft. Still, we can usefully categorize neurotransmitters according to their broadly different functions around the body:
In case you're interested in the structure of these neurotransmitters - perhaps because you are researching the effects of exogenous compounds ("drugs") on brain activity - here's a little more biochemistry:
Most of the videos above have focused on the neurotransmitter in the synaptic cleft. Naturally, the receptors on the post-synaptic neuron are critical to signaling. So let's take a slightly closer look at receptor types:
And finally, a little more detail on the importance of synaptic location, not just type, in determining the type of action produced by a neural circuit:
That should suffice as a basic introduction to neurotransmission for the bulk of fMRI experiments, where we are looking at the collective effects of millions of neurons and trillions of synapses in any given voxel. Additional videos suggested by YouTube should provide good branches for those of you wanting more detail.
At this point, I want to shift to looking at the axon structure and its myelin sheath because this is an important distinction at the level of the fMRI voxel. We will tend to categorize any given voxel as containing mostly white matter (myelinated axons) or mostly gray matter (cell bodies). We will look at these in turn.
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Post-publication bonus video! I came across this video on some recent discoveries on dendritic activity while hunting for introductions to myelin structure. It's well worth a watch.
