Core 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 material under each separate discipline. That might have worked. Indeed, it could still work if an appropriate group such as the OHBM education committee decides to have a go. But I'm going to try something different. To borrow a phrase from blockchain folks, I want to be permissionless. I'm going to try to collate publicly available material myself, with occasional assistance from others if and when I get proper stuck. Trying to do it all myself should provide me with an interesting set of learning experiences, I hope, and it should also help guarantee that anyone, anywhere with access to YouTube can participate.

So, how's this gonna go? Not sure, it's an experiment. I have the following main disciplines listed and as of now I plan on tackling them in this order (although I may well start on some of the later ones before finishing the earlier ones). I'm just gonna start and see what happens. I will aim for one post a week, equivalent to 1-2 hours of learning. As I go, I will do my best to organize the collection - for example, all will have Core curriculum somewhere in the title, plus appropriate labels - and once there are enough of them I'll create a main page with links; a virtual contents table.

Likely major themes, in likely order:

• How to learn from videos
• Mathematics
• Physics
• Engineering
• Biology
• Physiology
• Biochemistry
  
• Biophysics
• Image processing & analysis
• Statistics
• Psychology
• Experimental design
• Practical issues

Why this order? The logic is to try to build concepts on concepts. It's hard to understand most important engineering concepts without a decent understanding of some physics, which itself requires some decent understanding of certain mathematics, and so on. And, as noted in my Dec 2021 post, the goal here is to cover material that is non-volatile over decades. It's about the fundamental concepts, not the state-of-the-art. 

Right, enough preamble. Time to get going! 

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Infrequently asked questions:

Q: Where's your Twitter?  A: Gawn, all gawn. Got X'd out.

Q: Can we comment or make suggestions?  A: Yup. I'll do my best to answer comments to the posts, and my email still works.

Q: What do you mean by "non-volatile over decades?"  A: I'm taking my inspiration from the established sciences. Consider chemistry. Any chemist trained in a university anywhere in the world understands the Periodic Table and why the first row transition elements are different from the noble gases. They also understand carbon valence, pH, catalysis and hopefully some thermodynamics. These subjects are all fundamental to the field of chemistry and are unchanged whether they are learned in England, Sri Lanka or Venezuela. They also haven't changed fundamentally since I learned about them in the 1980s. 

Q: Why Blogger and not Substack or some newer platform?  A: Inertia. There's a dozen years of history on this site and a lot of it still applies. Indeed, I hope some of it will be getting re-used in the core curriculum! 

Q: Are you going to go back to more topical tips?  A: I don't have plans to, but if there's something important to cover then I may. However, I won't be going back to writing the series on fMRI artifacts or physiological confounds, at least not at this time. I'm focused on the fundamentals right now. Seeing way too many un(der)prepared folk still coming into neuroimaging.

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.

____________________

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.

QA for fMRI, Part 1: An outline of the goals

For such a short abbreviation QA sure is a huge, lumbering beast of a topic. Even the definition is complicated! It turns out that many people, myself included, invoke one term when they may mean another. Specifically, quality assurance (QA) is different from quality control (QC). This website has a side-by-side comparison if you want to try to understand the distinction. I read the definitions and I'm still lost. Anyway, I think it means that you, as an fMRIer, are primarily interested in QA whereas I, as a facility manager, am primarily interested in QC. Whatever. Let's just lump it all into the "QA" bucket and get down to practical matters. And as a practical matter you want to know that all is well when you scan, whereas I want to know what is breaking/broken and then I can get it fixed before your next scan.


The disparate aims of QA procedures

The first critical step is to know what you're doing and why you're doing it. This implies being aware of what you don't want to do. QA is always a compromise. You simply cannot measure everything at every point during the day, every day. Your bespoke solution(s) will depend on such issues as: the types of studies being conducted on your scanner, the sophistication of your scanner operators, how long your scanner has been installed, and your scanner's maintenance history. If you think of your scanner like a car then you can make some simple analogies. Aggressive or cautious drivers? Long or short journeys? Fast or slow traffic? Good or bad roads? New car with routine preventative maintenance by the vendor or used car taken to a mechanic only when it starts smoking or making a new noise?

Sharing data: a better way to go?

On Tuesday I became involved in a discussion about data sharing with JB Poline and Matthew Brett. Two days later the issue came up again, this time on Twitter. In both discussions I heard a lot of frustration with the status quo, but I also heard aspirations for a data nirvana where everything is shared willingly and any data set is never more than a couple of clicks away. What was absent from the conversations, it seemed to me, were reasonable, practical ways to improve our lot.*  It got me thinking about the present ways we do business, and in particular where the incentives and the impediments can be found.

Now, it is undoubtedly the case that some scientists are more amenable to sharing than others. (Turns out scientists are humans first! Scary, but true.) Some scientists can be downright obdurate when faced with a request to make their data public. In response, a few folks in the pro-sharing camp have suggested that we lean on those who drag their feet, especially where individuals have previously agreed to share data as a condition of publishing in a particular journal; name and shame. It could work, but I'm not keen on this approach for a couple of reasons. Firstly, it makes the task personal which means it could mutate into outright war that extends far beyond the issue at hand and could have wide-ranging consequences for the combatants. Secondly, the number of targets is large, meaning that the process would be time-consuming.


Where might pressure be applied most productively?

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 Skyra

There is an EPI sequence in VD13 that has a real time update of the on-resonance frequency, i.e. one that is computed and applied TR by TR, to combat drift caused by gradient heating. There are apparently versions for fMRI and diffusion-weighted imaging. I don't have any detailed information but if you are working on a Verio or a Skyra it might be time to talk to your physicist and/or local Siemens rep.

2. Phase encode direction for axial and axial-oblique EPI

Siemens uses A-P phase encoding by default whereas GE uses P-A by default. Essentially, for axial (and axial oblique) EPI the A-P direction compresses the frontal lobe but stretches occipital lobe whereas P-A stretches frontal lobe and compresses occipital. Pick your poison. (See Note 1.) Test each one out by setting the Phase enc. dir. parameter on the Routine tab. To set P-A from A-P (default) first click the three dots (...) to the right of the parameter field and open the dialog box, then enter 180 <return> instead of 0. You will probably find that the parameter change doesn't "stick" for appended scans, so saving a modified protocol in the Exam Explorer is a way to ensure the default (A-P) doesn't get reinstated without you noticing. More details to come in the next version of my user training/FAQ document.

3. Another way to force a re-shim

In my last user training/FAQ document (and here) I gave a simple way to force the scanner to re-shim at any point, e.g. when you know or strongly suspect the subject may have moved, or between lengthy blocks as a way to maintain high quality data in spite of slow subject motion and scanner drifts. But there is another way to do it and from some basic tests it looks to be superior. Here's a shaky video of the procedure conducted on a Trio running Syngo MR B17 (see Note 2):

(The essential procedure is the same for later software versions, but the layout of the 3D Shim window is slightly different.)

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)

i-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 ways to change things. So, in part to force us to consider each limitation with more rigor, and in part to stimulate thought and even activity within the neuroimaging community towards a brighter future, we decided to start a new series of posts that we'll cross-reference on our blogs. This blog will focus on the hand-wavy, conceptual side of things while at MathematiCal Neuroimaging you'll find the formal details and the mathematics.

We have loose plans at the moment to address the following topics: magnetic field strength considerations, gradient coil design considerations, RF coil design considerations, pulse sequences, contrast mechanisms, and motion and motion correction. We're going to hit a topic based on our developing interests and the issues that our local user community brings to us, so apologies if your fave doesn't actually appear in a post for months or years to come.


"You wanna go where? I wouldn't start from here, mate."

Blogs seem like the perfect vehicle for idle speculation about a fantasy future. The issues and limitations are very real, however, so that's where we will initiate the discussions. Then, wherever possible, we will gladly speculate on potential solutions and offer our opinions on the solutions that seem apparent today. But we're not going to try to predict the future; we will invariably be wrong. That would also be beside the point. What we want to do is motivate researchers, engineers and scanner vendors to consider the manifold ways an fMRI scanner and fMRI methods might evolve.

Note that in the last paragraph I referred specifically to an "fMRI scanner." A moment's consideration, however, reveals that most of the technology used for fMRI didn't arise out of dedicated efforts to produce a functional brain imager per se. Instead, we got lucky. Scanners are designed and built as clinical devices (worldwide sales in the hundreds to thousands) and not research tools for neuroscience (worldwide sales in the tens per year for pure research applications). A typical MRI scanner has compromises due to expense, size of subjects, stray magnetic field, applicability of methods to (paid) clinical markets, etc. Other forces are at work besides the quality and utility of fMRI. And these forces can be a mixed blessing.

Thus, part of the motivation for writing this post series is to provoke consideration of alternative current technologies; hardware or methods that exist right now but for whatever reason aren't available on the scanner you use for fMRI. Perhaps there are simple changes that can benefit fMRI applications even if these changes compromise a clinical application. For some facilities, like mine, that would be an acceptable trade.


What's in a name?

On this blog I'll use the moniker i-fMRI to label these op-ed posts. You can interpret the i however you like. Mathematicians might want to consider an imaginary scanner. Engineers might want to consider an impractical scanner. (This variant happens to be my preference.) Economists and business types might think of an inflationary fMRI scanner, because it's likely that the developments we seek will only drive the cost up, not down. And you neuroscientists? Well, we hope you'll consider your ideal fMRI scanner.

(Apple, if you're reading this - too late. We already sold the i-fMRI trademark to some company in China. Sorry.)

New user training guide/FAQ

I've just uploaded a new user training guide/FAQ that we use at Berkeley to initiate newbies into the ways of the dark side. It is Siemens-specific, for a Trio/TIM.

As last time, the guide is a bit rough. Sorry for English-isms and typos. It's worth exactly what you pay for it. It's free. Use and abuse it however you like. It's a Word document so that you can reorder things, add your own notes, etc. I would appreciate constructive feedback, especially if you find mistakes or have suggestions to improve it, but there's no need to ask permission to use it, change it, replicate it, sell it...

The most recent version of the training guide/FAQ is available from this web page:

http://bic.berkeley.edu/scanning

Locate the file attachment towards the bottom of the page, it's called 3T_user_training_FAQ_08Mar2012.doc. The most recent contents and a list of changes since the last version (April, 2011) appear below.


Caveat emptor.

The document is only a component of user training, don't expect to learn how to scan by reading it! Rather, use the tips to extend your understanding, refine your experimental technique and so on. Note also that this document is for a Siemens TIM/Trio (with 32 receive channels) and running software VB17. There may be subtle or not-so-subtle differences for the Verio and Skyra platforms, for software VB15, VD11, etc. so keep your wits about you if you're not on a Trio with VB17!

You may have local differences, e.g. custom pulse sequences, that allow you to do things that contradict what you find in this user guide. Talk to your physicist and your local user group before taking anything you find in this guide/FAQ too literally.

Finally, you wont find many (any?) references in this guide/FAQ. It's for the training of newbies, not a comprehensive literature review! If you are seeking further information on something I mention in the guide and you can't find a suitable reference yourself, shoot me an email and I'll do my best to point you in a useful direction.

 --------------------------------------

Update Notes (8^th March, 2012):

• Updated with new operating modes available under software syngo MR version B17.

• General tweaks to improve readability.

• Further recommendations on using the 32-channel coil for fMRI.

• Added a description of the new AutoAlign procedure, AAHScout.

• Added a new section: “I have an existing protocol that uses the old AutoAlign (AAScout). How do I get and use the new AutoAlign (AAHScout)?”

• Added a new section: “I want to add a new acquisition and acquire exactly the same slices as this other EPI acquisition I just acquired. How do I tell the scanner to do that?”

• Extended the discussion on the relative merits of PACE versus using an offline realignment alone, in the section on the ep2d_pace sequence.

• Fixed a typo concerning the slice ordering for descending slices.

• Added a new section: “What is a field map and how does it fix EPI distortion?”

• Added a new section: “I want to try to fix my distortion with a field map. What do I need to acquire?”

• Updated the sections on partial Fourier for EPI, noting that Siemens simply zero fills the omitted portion of k-space rather than doing a conjugate synthesis.

• Extended checklists.

Terminology change: characterizing EPI artifacts

After considering the rest of the topics that I want to cover in the series of posts on EPI artifacts, I've decided to change the terms "static" and "dynamic" to "persistent" and "intermittent," respectively. I think the new terms better reflect the dominant temporal character of each artifact. The idea is to sort them based on whether they are likely to plague every frame of an EPI time series, or come and go.

Take external RF interference, for example. Say you fail to close properly the RF-sealed door to the magnet room and the door opens slightly during your scan, leading to RF contamination from "environmental" sources. In this instance the RF interference itself isn't likely to be static - it will vary with whatever sources of RF happen to be in your scanner environment - but it will persist (at some level) until the door is closed. With a good eye or some appropriate diagnostics it would be possible to show the persistence of the problem throughout an acquisition. Contrast this situation with a static electrical discharge somewhere within the scanner room; tiny sparks that cause a broad range of electromagnetic frequencies, including radiofrequencies. These can arise if the humidity of the magnet room air becomes too low. Depending on the source of the sparks, the humidity, etc. you might find that only one or two TRs of a time series are contaminated, or you could find the entire time series is affected. I will therefore characterize static electrical discharges as an intermittent artifact.

Pedants will spot that the first example can be modulated by the position of the magnet room door, rendering the artifact intermittent, while in the second example the propensity for static electrical discharges will persist as long as the source exists, while the humidity remains low, etc. So, yeah, in some ways the distinctions I'm making are subjective. FMRI, like life, is complicated! Still, I'm hopeful that a more practical characterization of artifacts will assist you in differentiating and diagnosing them when it matters: during your experiment. And once you're an expert you will find it easy to comprehend the nuances of temporal behavior, when my artificial distinctions will be all but irrelevant to you.

So, there you have it. I'll be going back to edit the existing posts in this series over the next couple of days. Apologies for any confusion the switch creates.

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.

New blog! MathematiCal Neuroimaging

 
My colleague, DS has begun a new blog, mathematiCal Neuroimaging, dedicated to exploration of the mathematical principles underlying neuroimaging methods. Here are some excerpts from the section labeled About:

As the name of the blog partially implies, the topic here will be the mathematics and physics of neuroimaging. In particular the focus will be upon functional imaging of the brain.

 The style of this blog will range from tutorial-like expositions of present functional neuroimaging technology to whimsical explorations of how we might create better functional neuroimaging technology.

An entry on parallel imaging has just been posted. See you over there!

Twitter. Damn.

@practiCalfMRI

I thought I could resist, I really did. (I've been off Facebook* for more than two years!) But when Neuroskeptic took the plunge in June I started thinking that maybe I should suck it up, too. I mean, Neuroskeptic blogs ten times more frequently than I do and he still has time to tweet.

Not sure exactly how it will go. I'm going to treat it as an experiment. I can guarantee that there won't be daily tweets let alone hourly ones. I'm not going to bring anyone's cellular network to its knees. But I do come across little things related to fMRI that aren't worth a full blog post. A micro-blog ought to fit the bill, eh? We'll see...

* Okay, so technically I am still on fb. I maintain an account so that I can post comments to websites, merge with other online media, etc. Turns out it's really, really hard not to have fb unless you don't mind registering separately for every online newspaper and music service yet invented. But I never actually look at my fb page, so I apologize if you have a "friend" request suspended somewhere in cyberspace.

Understanding fMRI artifacts

Introducing the series

The workhorse sequence for fMRI in most labs is single-shot gradient echo echo planar imaging (EPI). As we saw in the final post of the last series, EPI is selected for fMRI because of its imaging speed (and BOLD contrast), not for its ability to produce accurate, detailed facsimiles of brain anatomy. Our need for speed means we are forced to live with several inherent artifacts associated with the sequence.

However, in addition to the "characteristic three" EPI artifacts of ghosting, distortion and dropout, when we're doing fMRI we are more concerned with changes over time than with the artifact level of an individual image. So, in this series we need to assess the sources of changes between images, even if the images themselves appear to be perfectly acceptable (albeit subject to the "characteristic three").


What's the data supposed to look like?

It would be rather difficult for you to determine when something has gone wrong during your fMRI experiment if you didn't have a solid appreciation of what the images ought to look like when things are going well. Accordingly, I'll begin this series with a review of what EPIs are supposed to look like in a time series. We'll look at typical levels of the undesirable features and assess those parts of an image that vary due to normal physiology. This is what we should expect to see, having taken all reasonable precautions with the subject set up and assuming that the entire suite of hardware (scanner and peripherals) is behaving properly.

Good axial data will be the focus of the first post in the series. (Axial oblique images will exhibit qualitatively similar features to the axial slices I'll show.) In the second post I'll show examples of good sagittal and coronal data. Artifacts may appear quite differently and with dissimilar severity merely by changing the slice prescription, so it's important to keep in mind the anisotropic nature of many EPI defects. Motion sensitivity is also different, of course. Motion that was through-plane for an axial prescription is in-plane for sagittal images, for example.


Ooh, that's bad.  Is it...?

With a review of good data under our belts it will be time to look at the appearance of EPI when things go tango uniform. I will group artifacts according to their temporal behavior - either persistent or intermittent - and their origins - either from hardware, from the subject, or from operator error. You should then be able to understand and differentiate the various artifacts and be able to properly diagnose (and fix) them when it counts the most: during the data acquisition. Waiting until the subject has left the building before finding a scanner glitch is a bit like doing a blood test on a corpse. Sure, you might be able to determine that it was the swine flu that finished him off, either way he's dead. Our aim will be to do our “blood tests” while there is still a chance of administering medicine and perhaps achieving a recovery.

If Blogger designed bathrooms...

...you can bet they would insist on power outlets over the bathtub. And two in the shower. (You never know when your laptop might get low on battery.)

Until they move into the construction industry, however, we must content ourselves with their software design skills, such as this gem: 

The "Screw your career six ways from Sunday button," a.k.a. the Publish Post button, is carefully placed well away from any button that you might want to use on a repeated basis for other reasons entirely. This layout is cunningly designed for blogging highly contentious posts; the sort where in your draft you might write reminder notes to yourself. Like, say, "Make sure you reference Mike Dood's crappy article on neologisms. Utter bollox!" These notes are, like Tweets from a congressman to female college students, designed to be confidential. You don't want them accidentally distributed to three billion random strangers just because you pushed your finger on the click pad a little too far to the left after that second glass of red wine, for instance. (Yeah, picky I know.) And you'd rather Mike Dood - a colleague in your department - didn't know your true feelings on his work, either. *

Ah, Blogger. Bless. Did James Bond ever have to put up with this sort of crap from Q, I wonder? I don't recall the eject button ever appearing in between the seek button on the radio and the cigarette lighter. Not even on the Lotus Esprit. And I'm sure James would have pointed it out if it had. Not exactly the most robust design, to be honest. ("Ah! Country music! I can't handle that. Let's see what else we can get out here in...  Fuuuuuu...!")





* Recovering from accidental publication is as simple as rushing to the Edit Posts page and deleting the offending post, then starting again from scratch now that you have just trashed all your work, all the while praying that not too many people just got e-notified of your new post and managed to see it (and cache it!) before you were able to hit Delete.

Open letter to Blogger

Blogger, you suck. You utterly suck. You have some major bugs in your software which have caused me to waste inordinate amounts of time recreating posts that oscillate between draft and published status. And when I submit a technical help request I hear nothing. For weeks.

Just now I hit SAVE AS DRAFT on a published post. No big deal you would think, right? I simply went back and hit PUBLISH POST again. And voila! The post showed up on the blog still marked as having been published on Sunday 5th June.... Ah, except that now the post's *content* has reverted to a draft from before 15th May! This, even though I have the archive frequency set to "Daily" after tuifu (Google it) on Friday 13th May. WTF?????

Lucky for you, rather than get in my car and drive down to Mountain View to find out who is in charge of this fiasco, I have a backup of my own. So "all" I have to do is re-type the content and re-upload those images that your bug sought to send back into the ether. Doubly lucky for you, I have an extra few hours of time this morning, having canceled a meeting earlier on. So this isn't nearly the crisis that it could have been, and it is only mildly increasing my blood pressure.

Now that I know what a piece of crap your software really is, I shall be taking other remedial steps to avoid similar snafus in the future; such as never, ever actually publishing a draft with the same name as a real post. Instead, I shall create drafts with names like, oh "Draft," and then when I am ready to actually publish the post I shall create a brand new one, with the intended title, and push that puppy out there. I want to see you bite me in the ass then, Blogger. Come on, give it your best shot!

Love,

practiCalfMRI

Memorial to an old post

This used to be the post entitled "Physics for understanding fMRI artifacts: Part Four." I had so many problems getting the draft published that I decided I wouldn't risk deleting this actual post, even though I have changed the title and the content. Wherever this thing points inside the "cloud" at Blogger, I want to seal it off like a leaky nuclear reactor and leave it for eternity, hopeful that it will be unable to infect any subsequent posts once it's buried in metaphorical concrete.

The replacement post, "Physics for understanding fMRI artifacts: Part F(f)our" is here.

I hadn't realized til recently just how flaky cloud computing can be. Clearly xkcd is way ahead of me, as usual:

 The Cloud.

(Stolen with his blanket permission from xkcd.com)

Blogger bites

So it transpires that Blogger had a Friday the 13th moment and as they are attempting to restore users' accounts and comments they have managed to trash a lot of other drafts in the process. The fourth installment of background physics for fMRI artifact recognition is presently resembling the first few notes I made back in March. Sunday's near-finished version is in the ether somewhere, perhaps. Wish I'd known there was an ongoing problem, I'd have found something else to do that day.

I guess we get what we pay for. Still, this is a powerful lesson for cloud users generally. Don't rely on the cloud!!! Make your own backups!!!!!  I have pdf "backups" of all completed posts, I guess it's time to start copy-pasting my own backups as I go, too. Sigh. Opening beer.... :-|

Administrative Post: 19 April, 2011 (2/2)

Siemens users may be interested in a user training guide & FAQ that we use at Berkeley to initiate newbies into the ways of the dark side. (Using the Force is often the only way to get an fMRI experiment to work. What, you thought the f stood for functional? Ha!)

The guide is a bit rough - sorry for English-isms and typos - is updated fairly regularly based on popular misconceptions and the like, and is worth exactly what you pay for it. It's free. Use and abuse it however you like. It's a Word document so that you can reorder things, add your own notes, etc. I would appreciate constructive feedback, especially if you find mistakes or have suggestions to improve it, but there's no need to ask permission to use it, change it, replicate it, sell it...

The most recent version of the training guide/FAQ is available from this web page:

http://bic.berkeley.edu/scanning

Locate the file attachment towards the bottom of the page, it's called 3T_user_training_FAQ_19April2011.doc. The most recent contents appears below.

Caveat emptor.

The document is only a component of user training, don't expect to learn how to scan by reading it! Rather, use the tips to extend your understanding, refine your experimental technique and so on. Note also that this document is for a Siemens TIM/Trio (with 32 receive channels) and running software VB15. There may be subtle or not-so-subtle differences for the Verio and Skyra platforms, for software VB17, VD11, etc. so keep your wits about you if you're not on a Trio with VB15!

You may have local differences, e.g. custom pulse sequences, that allow you to do things that contradict what you find in this user guide. Talk to your physicist and your local user group before taking anything you find in this guide/FAQ too literally.

Finally, you wont find many (any?) references in this guide/FAQ. It's for the training of newbies, not a comprehensive literature review! If you are seeking further information on something I mention in the guide and you can't find a suitable reference yourself, shoot me an email and I'll do my best to point you in a useful direction.

--------------------------------------

User guide/FAQ contents (as of 19 April, 2011):

Administrative Post: 19 April, 2011 (1/2)

I have renamed the three posts entitled "Diagnosing artifacts in fMRI data: Part x" to be "Physics for understanding fMRI artifacts: Part x." I am developing new posts in the series and through post seven at least the content is all quite theoretical; I'm not actually discussing artifacts or showing data! (But don't worry, I'm limiting the content to the essential concepts required to understand and differentiate fMRI artifacts. It's not going to be an entire MRI physics course!)

Once I've concluded this background series of physics posts (there are another eight or nine posts to come) I'll start a new series that will be entitled something suitable for actual artifact recognition (with data!), along the lines of the original title of the series. Hopefully this re-categorization will allow future readers to establish suitable paths through the posts, when a strictly chronological path probably won't be the best one.