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FMRI data modulators 2: Blood pressure
If you conduct fMRI experiments then you'll have at least a basic understanding of the cascade of events that we term neurovascular coupling. When the neuronal firing rate increases in a patch of brain...
View ArticleCOBIDAcq?
WARNING: this post contains sarcasm and some swearing.(But only where absolutely necessary.)COBIDAcq, pronounced "Koby-dack," is the Committee on Best Practice in Data Acquisition. It is based on the...
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Monitoring gradient cable temperature
While the gradient set is water-cooled, the gradient cables and gradient filters still rely upon air cooling in many scanner suites, such as mine. In the case of the gradient filters, the filter box on...
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FMRI data modulators 3: Low frequency oscillations - part I
Low frequency oscillations (LFOs) may be one of the the most important sources of signal variance for resting-state fMRI. Consider this quote from a recent paper by Tong & Frederick:"we found that...
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FMRI data modulators 3: Low frequency oscillations - part II
In the previous post, I laid out four broad categories of low frequency oscillation (LFO) that arise in fMRI data. The first three categories are mentioned quite often in fMRI literature, with aliasing...
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Arterial carbon dioxide as an endogenous "contrast agent" for blood flow imaging
I nearly called this post Low Frequency Oscillations - part III since it closely follows the subject material I covered in the last two posts. But this is a slight tangent. Following the maxim "One...
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Using multi-band (aka SMS) EPI on on low-dimensional array coils
The CMRR's release notes for their MB-EPI sequence recommend using the 32-channel head coil for multiband EPI, and they caution against using the 12-channel head coil:"The 32-channel Head coil is...
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Using multiband-EPI for diffusion imaging on low-dimensional array coils
This is a continuation of the previous post looking at MB-EPI on a receive coil with limited spatial information provided by its geometry, such as the 12-channel TIM coil or the 4-channel neck coil on...
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Restraining the 32-channel coil
There has been a move towards custom head restraint in recent years. These devices are tailored to fit the subject in such a way that any movement of the head can be transmitted to the coil. It is...
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A core curriculum for fMRI?
Blimey. Judging by the reaction to my earlier Tweet, there's something to be done here. And it makes sense because fMRI has been around for thirty years yet seems to be as ad hoc today as it was at its...
View ArticleCore curriculum: An introduction
After much delay, I am finally going to start developing the core curriculum I suggested in December 2021. At that time, I imagined recruiting a group of 10-15 domain experts to provide the bulk of...
View ArticleCore curriculum: How to learn from videos
Make coffee, fire up YouTube, click, watch, go about your day. Not so fast! To actually learn the material you'll see, you will need a minimum of the lecture itself, some sort of reading around the...
View ArticleCore corriculum: Mathematics I - Linear algebra
What is linear algebra? To get us going, I'm going to use the excellent lecture series by 3Blue1Brown and do my best to add some MRI-related questions after each video. Hopefully the connections won't...
View ArticleCore curriculum: Mathematics II - Linear algebra (cont.)
Continuing the series on linear algebra using the lectures from 3Blue1Brown, we are getting into some of the operations that will become mainstays of fMRI processing later on. It's entirely possible to...
View ArticleCore curriculum - Mathematics: Linear algebra III
Now we start to think about transformations between dimensions, e.g. taking a 2D vector into a 3D space. Non-square matrices come up frequently in engineering and research applications, including fMRI...
View ArticleCore curriculum - Mathematics: Linear algebra IV
Before getting back to the lectures from 3Blue1Brown, try this part review, part preview:Now let's get back into the meaning with a little more detail. A9. The dot (or scalar) product The dot product...
View ArticleCore 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...
View ArticleCore curriculum - Mathematics: Linear algebra VI
A13. Eigenvectors and EigenvaluesLet'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...
View ArticleCoffee Break with practiCal fMRI
A new podcast on YouTubeWe 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...
View ArticleCore 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...
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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...
View ArticleCore 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...
View ArticleCore 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...
View ArticleCore curriculum - Cell biology: synapses and neurotransmitters
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...
View ArticleFunctional connectivity, ha ha ha.
If you do resting-state fMRI and you do any sort of functional connectivity analysis, you should probably read this new paper from Blaise...
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