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Exploiting Tanzania
So a massive helium reserve may have been found in Tanzania's Rift Valley. Wonderful. All the western headlines this morning have put a typically western spin on it. Hurrah! We are saved! We get to go...
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Starting points for SMS-EPI at 3 T: Part II
In an earlier post I presented three starting protocols for the CMRR version of SMS-EPI, referred to as the MB-EPI sequence here. I'll use italics to indicate a specific pulse sequence whereas SMS-EPI,...
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Respiratory oscillations in EPI and SMS-EPI
tl;dr  When using SMS there is a tendency to acquire smaller voxels as well as use shorter TR. There are three mechanisms contributing to the visibility of respiratory motion with SMS-EPI compared to...
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Motion traces for the respiratory oscillations in EPI and SMS-EPI
This is a follow-up post to Respiratory oscillations in EPI and SMS-EPI. Thanks to Jo Etzel at WashU, you may view here the apparent head motion reported by the realignment algorithm in SPM12 for the...
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Use of split slice GRAPPA (aka Leak Block) for SMS-EPI reconstruction
Accurate separation of the simultaneously acquired slices is one of the bigger limitations of the SMS-EPI method, compared to the processing used for conventional multislice EPI. The default SMS...
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"Power plots" of respiratory effects in EPI
This will be brief, a simple demonstration of the sort of features visible in a "Power plot" of an EPI time series. The goal is to emphasize that chest motion produces apparent head motion effects in...
View ArticleMajor sources of apparent head motion in fMRI data
As I mentioned yesterday, there is a tendency when reviewing the output of a volume registration ("motion correction") algorithm to attribute all variations to real head motion. But, as was...
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Fluctuations and biases in fMRI data
In my last post I summarized the main routes by which different forms of actual or apparent motion can influence fMRI data. In the next few posts, I want to dig a little deeper into non-neural causes...
View ArticleFMRI data modulators 1: Heart rate
It's 2027 and you are preparing to run a new fMRI experiment. Since 2023 you've been working on a custom 7 T scanner that was developed to mitigate several issues which plagued the early decades of...
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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...
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