Hiya Steve
Thanks so much for getting back to me - I did a little extra research after
emailing last night and it turns out I was looking in an older version of
the FSL manual so I guess point three doesn't really apply.
I just wanted to ask - in light of the fact that my experiments are
event-related, the design is the same across runs and participants (in that
I make the same contrasts and efficiency of these are quite similar although
timings are not because presentation of items is random and coded to
subsequent memory accuracy) and I get different things for % signal change
and PEs - would it be incorrect to use parameter estimate values to analyse
my data sets?
Cheers
Hilary
>>> Stephen Smith <[log in to unmask]> 30/11/2009 08:18 >>>
Hi,
On 29 Nov 2009, at 22:48, Hilary Watson wrote:
> Hi FSL users
>
> I have run a total of three fMRI studies for my PhD and I am in the
> process
> of re-analysing to write them up.
>
> A lot of my work requires extraction of effect sizes in different
> ROIs and
> then running stats on these values - generally I have run functional
> localisers to create functional ROIs and then queried subsequent
> memory
> effects across a variety of conditions against an active baseline
> condition
> within these.
>
> For example
>
> objects later remebered - active baseline
> objects later forgotten - active baseline
>
> I orginally extracted the PEs (betas) using Featquery, however I have
> recently come across some literature that suggests that you
> shouldn't use PE
> for your stats, instead you should use % signal change (that said I
> have
> seen plenty of recent published papers in decent journals that have
> used FSL
> PEs).
>
> First question is whether I can stick with PEs for my stats?
Sure - in many cases there's little difference anyway. All data is
normalised across the entire 4D dataset to have a fixed mean value, so
as long as comparable designs are used for all subjects there won't be
much difference. Either choice should be acceptable, and Featquery
makes it easy to do either, by turning the relevant button on or off.
> Secondly I have also extracted % signal change for my data and have
> already
> seen there is not a simple one to one mapping to PE. For two of my
> data
> sets the numerical patterns are pretty much the same but for another
> it only
> appears to have an effect on one of the contrasts I am interested in
> looking
> at. Surely if the baseline used to covert these %s is the same across
> conditions (within participants) why would these conversions have a
> greater
> effect on one contrast? Obviously if it ok for me to use PE then
> this is so
> much of an issue
This can happen, for example where a voxel has a fairly different mean
intensity to the brain as a whole (e.g. if it's on the edge of the
brain and hence partial-volumed between grey-matter and non-brain
matter) then PE and %change will be more different. Also, for some
contrasts the height of that contrast's 'effective regressor' (see our
NeuroImage paper on design efficiency) can be different from what you
might expect, particularly for more complex designs and differential
contrasts.
> Thirdly, I have checked the FSL Feat manual and it says that you
> cannot use
> the 'covert PE into % signal change' option in Featquery for event
> related
> designs (which all of my experiments are) as this assumes the height
> of the
> waveform is 1, which is only appropriate for blocked designs. Is
> there a
> simple way to calculate % signal change using my PEs - say a formula
> and
> somewhere I can extract a waveform height value?
Are you sure the manual says that? I'm not sure it does but I may be
missing something. For most event-related designs even the simple
conversion in Featquery is accurate enough; if you have a concern then
have a look at J Mumford's website/tool that looks at this issue more
thoroughly.
Cheers.
> I am desperately confused and there is quite a lot riding on this so
> any
> help at all will be greatly appreciated. Let me know if you need me
> to
> clarify anything.
>
> Thanks in advance
>
> Hilary
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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