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!
Showing posts with label Contents. Show all posts
Showing posts with label Contents. Show all posts

Thursday, April 16, 2015

Another way to find posts: The Winnower


Open access online science publisher The Winnower has made a huge leap in scientific publishing and now offers bloggers a way to assign a digital object identifier (DOI) to any post uploaded to their site. Once there, the post can be reviewed, etc. just like any other online paper. They will also be archiving soon via CLOCKSS. (See Note 1.) With a DOI plus archiving it means that a post (and any reviews) should be traceable in perpetuity. Very good developments!

I had the privilege of helping Josh, The Winnower's industrious founder and administrator, create a new publication category for Neuroimaging and then used my post on physiologic confounds as the first test case. The post now has its own DOI (DOI: 10.15200/winn.142919.97862 ) should you prefer that to a URL. I submitted via a Word document because I've found that Blogger will occasionally hide irrelevant HTML code that needs to be edited out by hand. This can be a problem if you're in the habit, as I am, of copy-pasting text (e.g. quotes from papers) into a blog post. There is a new facility that will submit directly from a blog but in my first test (using Blogger) there were some major formatting issues. Josh informs me that he will be adding a facility for the Blogger API eventually, but using Word as an intermediate step gives me a chance to clean up links to references and that sort of thing. I have plans to submit many other posts to The Winnower so please let me know either in the comments below, in a review on the The Winnower version of the post or via Twitter whether you encounter problems, have suggestions for improvements, etc. Also, do please consider submitting your own blog posts to The Winnower. Let's build the Neuroimaging category!

I was around for and involved in the nascent Web of the early '90s (see Note 2) and I distinctly remember NCSA's Mosaic, the Planet Earth Home Page virtual library, UC Irvine's online bookshop, and the Cambridge coffee pot. But the development of open, online publishing supported by social media like blogs and Twitter, as well as post-publication peer review (PubPeer and PubMed Commons), feels like a true revolution for science. I may be wrong but it feels like we will look back at the current period as a major change in the way we interact. It only took us two decades. Now, however, The Winnower is contributing disproportionately to our future. Thank you.

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Notes:

1.  I already archive my important blog posts at The Internet Archive's Wayback Machine. In addition to providing an invaluable service, the Wayback Machine is also a wonderful way to get nostalgic and kill a few hours :-/

2.  I had an online poster at NMR Poster95, the first e-poster meeting of folks doing NMR and MRI. The front page of the poster got archived but the clickable poster itself is now defunct, I'm afraid. The wonderful Internet Archive does have other pages from my website at the time, however. They began archiving in 1996, and the earliest copy of my old website dates from January, 1997. Thank you, Internet Archive! There is also a summary of the first two NMR e-poster conferences in this paper from 1997.

Wednesday, September 19, 2012

Understanding 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 published.


Understanding fMRI artifacts

An introduction to the post series, defining what we mean by "good" data, and general discussion on viewing and interpreting EPI artifacts in a time series.



Good data


Understanding fMRI artifacts: "Good" axial data

Includes cine loops through time series EPI and statistical images to evaluate the data.


Understanding fMRI artifacts: "Good" coronal and sagittal data

Includes cine loops through time series EPI and statistical images to evaluate the data. (The notes include a description of the slice-dependent gradient switching limits that can prohibit certain slice orientations.)



Common persistent EPI artifacts


Common persistent EPI artifacts: Aliasing, or wraparound

Aliasing effects in the frequency and phase encoding dimensions.


Common persistent EPI artifacts: Gibbs artifact, or ringing

The origin of the ringing problem and demonstrations in phantom and brain data.


Common persistent EPI artifacts: Abnormally high N/2 ghosts (1/2)

Thursday, February 16, 2012

Physics for understanding fMRI artifacts: CONTENTS

Figured it might be useful to have some summary/contents pages. I'll do similar admin posts as the other series mature, too. And I will label these pages with "Contents" to make them easier to find via the sidebar.


Part One

An introduction to the series, followed by an introductory video courtesy of Sir Paul Callaghan: What is NMR and how does it work?


Part Two

Further videos explaining the principles of nuclear magnetic resonance - how the intrinsic spin of certain atomic nuclei interacts with applied magnetic fields to yield useful information.


Part Three

Videos showing the anatomy of a miniature scanner, a basic NMR experiment, why shimming is important for NMR (and MRI), how and why a spin echo works, and the relaxation of spins back towards their ground state.


Part Four

Mathematics of oscillations: an introduction to imaginary and complex numbers, and frequency and phase.