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!

Thursday, May 23, 2024

Core curriculum - Cell biology: the neuron's action potential


The last post reviewed the origins and properties of the resting membrane potential. Specifically, we are most interested in the membrane potential of neurons because they have an activated state that leads to signaling between neurons. Signaling from one neuron is achieved via an action potential from the cell body (soma) down its axon to synapses with other neurons. There are several good summary videos available online. Try them all to reinforce your knowledge.

Finally, in this post we get our first real look at synapses and excitatory and inhibitory neurotransmitters as part of a graded potential:

Now that you've seen the electrochemical action potential, in the next couple of posts we can dig more into neuron-neuron signaling, including synapses and the role of chemical neurotransmitters.


BONUS: a speedy review. All familiar stuff now, right?

Sunday, May 19, 2024

Core curriculum - Cell biology: cell membranes and the resting potential


A lot of the important functions of neurons (and glia) happen at their cell membranes. In the case of neurons, in addition to the membrane around the cell body (the soma), we also need to understand what happens along the neuronal processes (aka neurites): the dendrites (inputs) and the neuron's axon (the output). 

Let's begin this section by reviewing the structure of the cell membrane.



Transport across the cell membrane was introduce above. There are different mechanisms of membrane transport, each establishing certain behaviors of a cell.

The sodium-potassium pump is one of the most important membrane transport mechanisms for neural signaling. Let's take a closer look.


The cell's resting membrane potential was mentioned in the last two videos. The resting potential is an important starting point for understanding neuronal signaling via action potentials. For the last part of this post, we will look in more detail at the origins of the electrical potentials and electrostatic gradients across a cell membrane at rest.

In the next post we can start to look at cell signaling. Specifically, we are most interested in a neuron's action potential, which is the main way neurons communicate with each other.


Sunday, April 21, 2024

Can we separate real and apparent motion in QC of fMRI data?


A few years ago, Jo Etzel and I got into a brief but useful investigation of the effects of apparent head motion in fMRI data collected with SMS-EPI. The shorter TR (and smaller voxels) afforded by SMS-EPI generated a spiky appearance in the six motion parameters (three translations, three rotations) produced by a rigid body realignment algorithm for motion correction, such as MCFLIRT in FSL. The apparent head motion is caused by magnetic susceptibility variations of the subject's chest as he/she breathes, leading to a change in the magnetic field across the head which, in turn, adds a varying phase to the phase-encoded axis of the EPI. This varying phase then manifests as a translation in the phase-encoded axis. It's not a real motion, it's pseudo-motion, but unfortunately it is a real image translation that adds to any real head motion. I should emphasize here that this additive apparent head motion arises in conventional multi-slice EPI, too, but it's generally only when the TR gets short, as is often the case with SMS-EPI, that the apparent head motion can be visualized easily (as a spiky, relatively high frequency fluctuation in the six motion parameter traces). In EPI sampled at a conventional TR of 2-3 sec, there are only a small handful of data points (volumes) per breath for an average breathing rate of 12-16 breaths/minute and this leads to aliasing of most of the apparent head motion frequency. It may still be possible to see the spiky respiration frequency riding on the six motion parameters, but it's not always there as it is for TR much less than 2 seconds.

Once we'd satisfied ourselves we'd understood the problem fully, I confess I let the matter drop. After all, we have tools like MCFLIRT that try to apply a correction to all sources of head motion simultaneously, whether real or apparent. But now I'm wondering if we might be able to evaluate the real and apparent motion contributions separately, with a view to devising improved QC measures that can emphasize real head motion over the apparent head motion when it comes to making decisions on things like data scrubbing. Jo has been dealing with the appropriate framewise displacement (FD) threshold to use when including or excluding individual volumes. (See also this paper.)

Let's review one of the motion traces from my second 2016 blog post on this issue:

These traces come from axial SMS-EPI with SMS factor (aka MB factor ) of 6. The x axes are in seconds, corresponding to TR = 1 sec. (The phase-encoded axis is anterior-posterior, which is the magnet Y direction.) On the left is a subject restrained with only foam, on the right the same subject's head is restrained with a printed head case. During each run the subject was asked to take a deep breath and sigh on exhale every 30 seconds or so. We clearly see the deep breath-then-sigh episodes in both traces, regardless of the type of head restraint used. Yet it is also clear the apparent head motion, which is the high frequency ripple, dominates the Y, Z and roll traces on the left plot. On the right plot, the dominant effect of apparent head motion manifests in the Y trace, with a much reduced effect in the roll axis. Already we are seeing a slight distinction between the translations and rotations for apparent head motion. It looks like apparent head motion contributes more to translations than rotations, which makes sense given the physical origin of the problem. In which case, can we assume that by extension real head motion will dominate the rotations?

For now, let's assume that the deep breath-then-exhale episodes are producing considerable real head motion, in addition to the large apparent head motion spike from exaggerated chest movement. The left plot above shows that pitch, yaw and roll all characterize the six deep breaths readily. They are also visible in Z and X, but with considerably reduced magnitude. There's no clear effect in the Y trace which is dominated by the aforementioned apparent head motion. So far so good! When the head can actually move in the foam restraint, we have clear biases towards rotations for real head motion and translations for apparent head motion. 

What about the right plots? Real head motion is far harder to achieve because of the printed head case restraint. But we assume the apparent head motion is basically the same magnitude because it's chest motion, not head motion. So we might think of this condition as being a low (or lowest) real motion condition. As with the foam restraint on the left, we again see Y translations dominated by apparent head motion. The roll axis also displays considerable apparent head motion. And as for the foam restraint, the roll and pitch axes display something that may be real or apparent head motion for each of the deep breath-then-exhale periods. We can't be sure if the head (or the entire head case, or even the entire RF coil!) was really moving during each breath, but let's assume it was. If so, then for good mechanical head restraint we have the same rough biases as for foam restraint in our motion traces: real motion dominates rotations, apparent motion manifests mostly as translations.

Jo sees a similar distinction between real and apparent head motion in the motion parameter plots of her 2023 blog post. In her top plot, which she suggests is a low real motion condition, the apparent motion dominates Y and Z translations and the roll traces, exactly as my example above. Her second plot exhibits considerable real head motion. The apparent head motion is still visible as ripples on the Y and Z translation traces, but now it's clear the biggest changes arise in the three rotations and these changes are probably real head motion. Again, we have real motion dominating rotations while apparent motion manifests more in the translations.

Finally, let's consider Frew et al., who looked at head motion in pediatrics. Here's Figure 3 from their paper:

Using framewise displacement (FD), they show a transition from FD dominated by translations to FD dominated by rotations when considering low, medium and high (real) head motion subjects. Rotations and translations are both affected significantly in the medium movement group. Still, the trend here suggests that we might consider rotations alone as an index of real head motion if, as suggested above, apparent head motion contributes mostly to translations.

So, what might we do to separately evaluate real and apparent head motion? This is where you come in. I only have one starting idea, and that's to shift to considering FD using only rotations, rather than rotations and translations, when setting thresholds for the purposes of QC and scrubbing. Based on what I've presented here, we might be able to set a threshold for FD(rotations only) that will capture most of the real head motion and have a much reduced dependency on apparent head motion. This measure could help avoid mischaracterizing large apparent head motions as events to reject when they are inherently fixable with MCFLIRT and similar. (Real head motion produces a big spin history effect and likely introduces non-linear distortions in the images.) Whether the reverse is true - that is, whether FD(translations only) captures most of the apparent head motion and a reduced contribution from real head motion - I leave as an exercise for another day, but my suspicion is that it is not. Put another way, I think the focus should be on using the rotations to capture and evaluate real head motion. Pooling translations and rotations in measures like FD may be complicating the picture for us.


Monday, April 15, 2024

Core curriculum - Cell biology: taxonomy


Most of the biology we need to learn can be treated orthogonal to the mathematics, whereas the mathematics underlies all the physics and engineering to come. As a change of pace, then, I'm going to start covering some of the biology so I can jump back and forth between two separate tracks. One track will involve Mathematics, then Physics, then Engineering, the other will be Cell Biology, Anatomy, Physiology and then Biochemistry.


Let's begin with a simple overview of cell structure:

The owner prohibits embedding this video in other media so you'll have to click through the link to watch.

Next, a little more detail on what's in a typical mammalian cell:

All well and good, but we are primarily interested in the types of cells found in neural tissue, whether central nervous system (CNS) or peripheral nervous system (PNS):

A little more taxonomy before we get into the details of neurons and astrocytes. In this video, we start to encounter the chemical and electrical signaling properties in cells, something we will get into in more detail in a later post. Still, it's timely to introduce the concepts.

As we move towards the neural underpinnings of fMRI signals, we need to know a lot more about neurons and astrocytes. Let's do neurons first.

While this next video repeats a lot of what you've already seen, there is enough unique information to make it worth watching.

Finally, a little more taxonomy that relates types of neurons to parts of the body, something that could be very important for fMRI when we are considering an entire organism.

To conclude this introduction to cell biology and types of neural cells, let's look at glial cells in more detail.

 Another simple introduction, to reinforce the main points:

And a nice review to wrap up.

We will look far more closely at astrocytes in a later video, once we've learned more about blood flow and control. For now, just remember that those astrocyte end feet are going to be extremely important for the neurovascular origin of fMRI signals.


That will do for this primer. The next post in this series will concern the resting and action potentials, signaling and neurotransmission.


Thursday, April 11, 2024

Coffee Break with practiCal fMRI

 A new podcast on YouTube

We all know the best science at a conference happens either during the coffee breaks or in the pub afterwards. This being the case, practiCal fMRI and a guest sit down for coffee (or something stronger) to discuss some aspect of functional neuroimaging in what we hope is an illuminating, honest fashion. It's not a formal presentation. It's not even vaguely polished. It’s simply a frank, open discussion like you might overhear during a conference coffee break.

In the inaugural Coffee Break, I sit down with Ravi Menon to discuss two recent papers refuting the existence of a fast neuronal response named DIANA that was proposed in 2022. Ravi was a co-author on one of the two refutations. (The other comes from the lab of Alan Jasanoff at MIT.) We then digress into a brief discussion about the glymphatic system and sleep, and finally some other bits and pieces of shared interest. I've known Ravi for three decades and it's been a couple of years since we had a good natter, so we actually chatted on for another hour after I stopped recording. Sorry you don't get to eavesdrop on that conversation. It was all science, zero gossip and the subject of expensive Japanese whisky versus Scotch and bourbon did not feature, honest guv.


All the links to the papers and some items mentioned in our discussion can be found in the description under the video on YouTube. 

What's next for Coffee Break? I have a fairly long list of subject matter and potential guests. I'm hoping to follow some sort of slightly meandering theme, but no promises. I'm also hoping to get new episodes out about once every couple of weeks. But again, no promises.

(PS The series of posts on the core fMRI syllabus will resume shortly with a new branch on biology, starting with basic cell biology.)


Saturday, March 9, 2024

Core curriculum - Mathematics: Linear algebra VI


A13. Eigenvectors and Eigenvalues

Let's end this section on linear algebra with a brief exploration of eigenvectors and their eigenvalues. An eigenvector is simply one which is unchanged by a linear transformation except to be scaled by some constant. The constant factor (scalar) by which the eigenvector is scaled is called its eigenvalue. If the eigenvalue is negative then the direction of the vector is reversed as well as scaled.

 Curious about the terminology? Eigen means "proper" or "characteristic" in German. So if you're struggling to understand or remember what eigenvectors are all about, perhaps it helps to rename them "characteristic vectors" instead.

Here's a nice introduction to the concepts. Pay close attention to the symmetry arguments. It turns out eigenvectors represent things like axes of rotational symmetry and the like:



And with some of the insights under your belt, here's a tutorial on the mechanics of finding eigenvalues and eigenvectors:



Thursday, February 22, 2024

Core curriculum - Mathematics: Linear algebra V


With some understanding of basic matrix manipulations, we're ready to begin using matrices to solve systems of linear equations. In this post, you'll learn a few standard tools for solving small systems - system defined by a small number of equations - by hand. Naturally, larger systems as found in fMRI will use computers to solve the equations, but you should understand what's going on when you push the buttons.

A11. Elementary row operations and elimination

This is just your standard algebraic manipulation to solve multiple simultaneous equations, e.g. dividing both sides of an equation by some constant to be able to simplify, but where the equations are represented as matrices:


A12. Cramer's Rule for solving small linear systems

According to Wikipedia:

In linear algebra, Cramer's rule is an explicit formula for the solution of a system of linear equations with as many equations as unknowns, valid whenever the system has a unique solution. It expresses the solution in terms of the determinants of the (square) coefficient matrix and of matrices obtained from it by replacing one column by the column vector of right-sides of the equations.