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fMRI software bugs could upend years of research

theregister.co.uk

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Re: fMRI software bugs could upend years of research

#111

Post by Retric »

bad_user wrote: post #94
Retric wrote: post #86

Earlier quoted context omitted.

Interestingly one of the best arguments apposed to free will is people being terrible random number generators. Which tends to be hand waved away. Which suggests people have already decided which side they believe in and only try and rationalize it after the fact. ;)

I've never heard of that argument, though I admit I'm new to this discussion. But, given that people can and have built pretty good random generators, by finding sources of entropy and even with pure math, thus sidestepping our limitations, the point is kind of moot IMHO.

The logic is odd but strait forward. Basically, free will requires people to make choices independent of the past state of the universe. Aka if you replayed to universe up to this point several times they would not always respond in the same way.

If that's the case people should be able to make unpredictable choices by definition. However, when asked to be unpredictable they fail. So, at best people have a limited form of free will.

PS: This is something of an upper bound. At the other end, if replaying someone's life they only have a single non predictable choice they they may have free will. Similarly if they make the same choices in a very large number of universes and only make a different choice in one you could still argue that that's free will. But, the lower bound is not that meaningful of a distinction.

Re: fMRI software bugs could upend years of research

#112

Post by clord »

acqq wrote: post #56
randcraw wrote: post #44

As someone who works in the biomedical imaging business and is also a fan of philosophy, I think this news will matter more to folks in the latter camp. For a couple years now philosophers have insisted that fMRI images prove there is no such thing as free will. Today's revelation should put an end to that whole line of reasoning (and the absurd amount of fatalism that it engendered). (The back story: Apparently fMRI…

Free will as in "there's something that can't be explained by chemistry and electrical signals in the brain" is just an attempt of some believers to rationalize their belief in the kind of the supernatural "soul."

Are you suggesting there is no room for quantum effects in the brain? Honest question because I thought determinism is out of fashion now-a-days for that reason.

Re: fMRI software bugs could upend years of research

#114

Post by nkurz »

pfooti wrote: post #84

The dead salmon study seems relevant here in discussion of how fMRI is used, especially the theory -ladenness of observations. http://blogs.scientificamerican.com/scicurious-brain/ignobel...

Maybe I missed the link, but the full text of the readable, relevant, and enjoyable article that blog post discusses is here:

The principled control of false positives in neuroimaging

Bennett, Wolford, Miller 2009

http://scan.oxfordjournals.org/content/4/4/417.full

Re: fMRI software bugs could upend years of research

#115

Post by mattkrause »

nonbel wrote: post #102
mattkrause wrote: post #97

Earlier quoted context omitted.

Maybe we're agreeing? The ENTIRE POINT of the paper is that there are inappropriate assumptions baked into the defaults of FSL and SPM. (AFNI has an actual code-does-the-wrong-thing bug). These errors result in cluster-wise tests being inappropriately sized: when thresholds are set to p They tested this by dividing a single stream of "off" data into segments of "ON" and "OFF" data. They do this in four different ways…

I think we are largely in agreement on the surface. The problem is that they are attributing the "positive" results to statistical error, when it isn't due to that. The stats are working just fine and correctly telling us the null hypothesis is false. The problem is with the crappy null hypothesis, not the stats.

The experiment is set up so that there are no true positives.

When the threshold is pAre you trying to say that it's not the t-test per se, but something before it in the pipeline? If so, sure, of course, but that's not the null. The null is that chunks randomly labeled as ON are the same as chunks randomly labeled as OFF, and since it's not physically possible for the labels to affect the signal, this null must be true.

Re: fMRI software bugs could upend years of research

#116

Post by waqf »

strictfp wrote: post #58
iLoch wrote: post #19

" How X looks like" -- what's with this gramatical mistake? I see it everywhere. Is it a regional thing?

It's a common error for native Swedes, It's a direct translation from Swedish. Could be true for other languages as well, I believe most Germanic languages use "how".

English uses "how" too: it's correct to say "how X looks", with no "like".

"what … like" is synonymous with "how".

Re: fMRI software bugs could upend years of research

#117

Post by nerdponx »

"Further: “Our results suggest that the principal cause of the invalid cluster inferences is spatial autocorrelation functions that do not follow the assumed Gaussian shape”."

This has nothing to do with bugs and everything to do with bad statistical analysis. It's Google Flu all over again.

Re: fMRI software bugs could upend years of research

#118

Post by Retra »

threatofrain wrote: post #63
randcraw wrote: post #44

As someone who works in the biomedical imaging business and is also a fan of philosophy, I think this news will matter more to folks in the latter camp. For a couple years now philosophers have insisted that fMRI images prove there is no such thing as free will. Today's revelation should put an end to that whole line of reasoning (and the absurd amount of fatalism that it engendered). (The back story: Apparently fMRI…

There's free will as in a decision-making system that generates different options and selects one based on constraints, which is something a computer can do, and then there's free will as in the ability to defy the mechanics of one's biophysics, which is just an indirect way of saying metaphysical soul. I don't think empiricists can even discuss the kind of free will which defies causal explanation, the kind of mind…

Free will is just the sensation of having a brain that models counterfactuals. It allows you to have emotions like hope and regret, since you are capable of imagining the world being different from how it is. It allows you to understand your role in the consequence-that-is-the-current-reality.

And here there's nothing to debate. Of course free will exists. It exists just like every other aspect of mental perspective exists. Nobody is debating whether love, hunger, confusion, or boredom exist just because they aren't quantified and modeled in a properly predictable manner. They're debating free will because religious people want a common experience and a long history of unaddressed confusion to leverage for their self-comfort. A "mystery" that not even scientists can touch.

Re: fMRI software bugs could upend years of research

#119

Post by Retra »

clord wrote: post #112
acqq wrote: post #56

Earlier quoted context omitted.

Free will as in "there's something that can't be explained by chemistry and electrical signals in the brain" is just an attempt of some believers to rationalize their belief in the kind of the supernatural "soul."

Are you suggesting there is no room for quantum effects in the brain? Honest question because I thought determinism is out of fashion now-a-days for that reason.

Determinism and non-determinism are both just models that can be converted into each other fairly easily. Either way, that has nothing to do with free will, because getting random outcomes is not 'will' at all, let alone free will -- as ill-defined as that concept is.

Re: fMRI software bugs could upend years of research

#120

Post by dewarrn1 »

bpchaps wrote: post #103
jballanc wrote: post #78

The real takeaway lesson from this research should be the vital importance of Open Data to the modern scientific enterprise: > "lamentable archiving and data-sharing practices" that prevent most of the discipline's body of work being re-analysed. Keeping data private before publication is (at this point in time) understandable. Once results are published, however, there is no excuse for not depositing the raw data in…

Yeah, it's pretty frustrating. I tried getting my own data from an fMRI study, but was told that the signed paperwork specifically disallowed this sort of thing. Not even my doctor could request it. The only option I have is to completely withdrawal myself from the study, but that would be a pretty dick move. The other option is to wait until next year when the study's wrapped and then request it. Though, I'm not eve…

I completely agree that this can be frustrating. For what it's worth, the data from a research study aren't necessarily going to be clinically informative to a GP or even to a radiologist. Structural MRI data could potentially be interpreted, but the sequences collected for research are still different than what you'd get if you went in for a clinical scan.

And if you're interested in having the data for your own purposes, there may still be some liability concerns for the researchers. There's always an agreement to keep MRI data under strict supervision to avoid leaks of personal health information, so providing those data to participants (safeguards or no) could potentially count as a breach of protocol.

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