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Common intermittent EPI artifacts: Subject movement
More fMRI experiments are ruined by subject motion than any other single cause. At least, that is my anecdotal conclusion from a dozen years' performing post-acquisition autopsies on "bad" data. The...
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The 3 T gets a new home
After a very long wait that spanned two prefabricated buildings - we weren't supposed to call them trailers, some sort of negative connotation - the Henry H. Wheeler, Jr. Brain Imaging Center took its...
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Physics for understanding fMRI artifacts: Part Thirteen
A tour through a real EPI pulse sequence In some posts I've got planned it will be important for you to know something about all of the different functional modules that are included in a real EPI...
View ArticleSiemens slice ordering
I've heard on the wind that there is still confusion or even a total lack of awareness of the change in slice ordering for interleaved slices when going from an odd number to an even number of slices,...
View Articlei-fMRI: Introducing a new post series
My colleague, MathematiCal Neuroimaging and I have been discussing what we see as flaws or limitations in current functional MRI scanners and methods, and what the future might look like were there...
View ArticleMethods reporting in the fMRI literature
(Thanks to Micah Allen for the original Tweet and toCraig Bennett for the Retweet.)If you do fMRI you should read this paper by Joshua Carp asap:"The secret lives of experiments: Methods reporting in...
View Articlei-fMRI: Prospective motion correction for fMRI?
An ideal fMRI scanner might have the ability to update some scan parameters on-the-fly, in order to reduce or eliminate the effects of subject motion. Today, this approach is commonly referred to as...
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Intense stray (static) magnetic field gradients may affect cognition
Have you ever wondered whether it's appropriate to put a research subject into a dark, confined tube that makes an awful din, whereupon the subject may learn that his brain has some abnormality, and...
View ArticleUnderstanding fMRI artifacts: CONTENTS
An organizational post I'd been meaning to get to for a while. There are some posts to come in this series, in parentheses below. I'll update this page with links as these posts get...
View ArticleWe're arXiving! (Another post on GRAPPA.)
In another move to accelerate the development of methods for neuroimaging applications, some colleagues and I recently decided to abandon a second attempt to publish a paper in traditional journals and...
View ArticleQuench!!!
I was persuaded by Tobias Gilk to post a video of the quench of Berkeley's old 4 T magnet, a fairly momentous event that a lot of people have enjoyed watching in private (whether they were absent or...
View ArticleIntroduction to MR principles: online resources
I recently came across some extremely informative online resources for learning the basics of (nuclear) magnetic resonance. The first (via Agilent's Spinsights.net blog) is an online simulator that is...
View ArticleNext-gen platforms for evaluating scientific output
Tal Yarkoni has a paper out in Frontiers in Neuroscience, "Designing next-generation platforms for evaluating scientific output: what scientists can learn from the social web." As someone who has...
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Draft checklist for fMRI methods reporting in the literature
It took a little longer to get to than I'd planned, but contained in this post is a first pass at a checklist for acquisition parameters that I think should be included in the methods section of fMRI...
View ArticleMotion problems in fMRI: Receive field contrast effects
Motion has been identified as a pernicious artifact in resting-state connectivity studies in particular. What part might the scanner hardware play in exacerbating the effects of subject motion?My...
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Review: Using a bias field map to improve motion correction of EPI time series
In a new paper entitled "Effects of image contrast on functional MRI image registration,"Gonzalez-Castillo et al. evaluate the performance of motion correction (a.k.a. registration) following a...
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Review: Differentiating BOLD from non-BOLD signals in fMRI time series using...
Disclaimer: I'm afraid I haven't done a very good job reviewing the entirety of this paper because the stats/processing part was pretty much opaque to me. I've done my best to glean what I can out of...
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Inadequate fat suppression for diffusion imaging
Diffusion imagingis often included as a component of functional neuroimaging protocols these days. While fMRI examines functional changes on the timescale of seconds to minutes, diffusion imaging is...
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A checklist for fMRI acquisition methods reporting in the literature
This post updates the draft checklist that was presented back in October. Thanks to all who provided feedback. The updated checklist, denoted version 1.1, incorporates a lot of the suggestions made...
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Quick update for Siemens users
Apologies for the lengthy absence. Many irons in the fire, etc. So until I can provide a more considered post I give you these three random tidbits:1. Syngo MR version D13 for Verio and SkyraThere is...
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