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!

Friday, June 10, 2011

If Blogger designed bathrooms... 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!