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!

Tuesday, May 31, 2011

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.)

Wednesday, May 18, 2011

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.... :-|

Wednesday, May 4, 2011

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.