Thanks for this question, this gives me an opportunity to ask something
related I was often wondering about.
First a remark to your question. Why do you want to bias correct your 4D
data? This would correct for (static) differences of the signal
intensity over the brain. But when collecting functional data you are
interested in the BOLD signal fluctuations, not the static bias, hence I
doubt that you gain anything with a bias correction. I would even
assume, that this is likely to introduce some problems. In my opinion,
the susan smoothing copes somehow with the bias problem on a local
scale. However, if you have got non-BOLD signal fluctuations over time
(e.g. B0 fluctuations, physiological artefacts) you might be interested
to correct for these. Anyway, I am not an FSL expert, so I hope that the
expert will come up with some more competent comments on this issue.
My follow-up question here is related to the consequences of a signal
bias on statistical maps. If there is a strong gradient in the data
(macaque data, surface coil), the SNR changes within the brain volume,
hence a common statistical threshold would result in biased maps, making
it more difficult to detect activity down the signal gradient. Should
this be accounted for when applying significance thresholds to the data?
In my case, detecting 'strong activations' in parietal and frontal
regions, but 'weak activations' in lower temporal regions might simply
be attributed to the signal gradient and not to the underlying
physiological processes. What is a common practice o cope with such a
Thanks for any comments,
On 06/20/2010 02:41 AM, R. Matthew Hutchison wrote:
> Hi FSL users,
> Is it common practice to bias correct the 4D EPI data?
> There doesn't seem to be an option in the FAST GUI to do this, so
> perhaps there are clear reasons not to.
> Any insight would be much appreciated.
> R. Matthew Hutchison
> R. Matthew Hutchison, PhD. Candidate
> Centre for Functional and Metabolic Mapping
> Robarts Research Institute
> Cuddy Wing - 9.4T Suite
> P.O. Box 5015, 100 Perth Drive
> London, Ontario, Canada N6A 5K8