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.

Physics for understanding fMRI artifacts: Part F(f)our

(Wondering why the title has F(four) in it? It's so that Blogger can't trash this post for a third time! I'm giving it a new, unique name. Ha!)

It's finally time to get back to the series of posts on the essential physics concepts that will allow you to interpret and differentiate between acquisition artifacts. There are another five or six posts in this background series, so bear with me. After that we will shift gears and look at "good data," taking some time to assess the normal variations that you can expect to see in time series EPI, and then I promise we'll look at artifacts themselves.


When reality meets imagination

Before we go any further there are a few mathematical properties we need to review. These are actually quite simple relationships that, for the most part, can be explained via a handful of pictures. Like this one....

Maths dude, chillin'.

Complex numbers

The name notwithstanding, complex numbers are quite straightforward to understand from a physical perspective, with a tiny bit of explanation. By the time you've finished reading this post you should have a basic idea of what complex numbers mean and where they come from (they arise quite naturally, as it happens), but for now I am simply going to define some relationships. Hang in there.

We start by defining a so-called imaginary number as any number for which the square is negative. The squares of real numbers - the ones you're used to in everyday life, such as 2, 8.73, -7, pi, and so on - are always positive, whether the number being squared is positive or negative. Thus 2x2 = 4, 8.73x8.73 = 76.2129, -7x-7 = 49 and so on. Squaring a negative number results in a positive number. So how could we possibly get an answer of -4 or -25 out of any square?

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)

Resting state fMRI: just what can we allow subjects to do?

I'm still waiting to see if Google/Blogger might recover the draft of that fourth post in the series on background physics for fMRI artifact recognition, so in the mean time I thought I'd take a closer look at the only part of the resting-state experiment that I didn't address in detail over the past few months: what we allow the subjects to do during the acquisition.

Potayto, potahto

I'd like to begin with a definition change to assist in understanding the limits of "resting state" fMRI. I'll continue to refer to rs-fMRI as the act of acquiring a block of fMRI data - let's say six minutes' worth - in the absence of any specific externally presented task during the acquisition, with one small exception: we'll assume that the subject is presented with a simple fixation cross and is asked to keep his eyes open. (More on visual and auditory effects on rs-fMRI below.)

Now, though, I'd like to rename the mental activity that is happening during the rs-fMRI acquisition period. The definition of "rest" is tricky because it depends on so many state-dependent factors. What if I'm worried about an upcoming exam? What if I'm hungry and distracted by the need for food? Just because I'm awake during both doesn't make them equivalent periods of "rest," even if I am lying in the scanner staring at a fixation cross in both cases. And, because I want to distinguish between such periods without an explicit task in the discussion to follow, I'm going to term what we do today as "free-thinking state" fMRI, a term used by Cindy Lustig from WashU in a  2003 interview about some of her work.

Okay, so now we have a new definition to work with. How might this state of free thinking be manipulated without fundamentally changing the goal, which is (I assume) to map the largest networks that arise intrinsically, in the absence of explicit, externally driven, goal-directed behavior (in the form of some sort of task presentation)?


Caveats: every fMRI experiment should have some!

Before we look at intentional manipulation of a subject's brain state, let's first review the confounds and limitations that have already been unearthed when it comes to conducting free-thinking state fMRI experiments. These are effects that have been shown to change the networks detected in standard rs-fMRI experiments. (See Note 1.)

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.... :-|

Using GRAPPA for fMRI in the presence of subject motion

I've received a few queries about my opinions on the use of GRAPPA for EPI time series, opinions which have been mentioned in passing in earlier posts. In my user training guide/FAQ are some sections that deal with GRAPPA features and performance, but I didn't include an in-depth illustration of the artifacts or the motion sensitivity. So, to help you make a decision on whether GRAPPA is something you should be using in your fMRI experiments, I'm going to post here a few more images and some movies to highlight the problems that can arise in the presence of significant head motion. I'll focus on R=2 accelerated EPI, but the principles hold for higher acceleration factors as well.

Whether or not you ultimately select GRAPPA for your experiment, it is important to make your determination objectively, taking into account your experimental needs, the benefits of the method, its failure modes and prior studies you can rely on for validation. (See "Beware of physicists bearing gifts!")

** Please note that the following information pertains to the GRAPPA implementation available as product on the Siemens Trio/TIM platform with VB15 software. If you have a different Siemens platform or a different vendor's scanner there may be significant differences in the implementation. **

A brief review of the GRAPPA method

If you don't have even a rudimentary understanding of parallel imaging (PI) generally or the GRAPPA method specifically, I would encourage you to stop reading this post now and go read at least one of these articles: Larkman & Nunes (2007) or Blaimer et al. (2004). Then come back when you're ready to proceed with a speedy review.