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FSL  May 2012

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Subject:

Re: Round 2: Change in functional connectivity between pre- and post-conditions using randomise

From:

Tom Johnstone <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 11 May 2012 16:40:00 +0200

Content-Type:

text/plain

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Agree with Dianne - a more informative set of questions would be hard to find!

I think the subtracting z-score maps should work fine - as you say,
they are a measure of connectivity, so subtraction will yield change
in connectivity maps, which can then feed straight into randomise.

-Tom
Centre for Integrative Neuroscience & Neurodynamics
School of Psychology and CLS
University of Reading
Ph.  +44 (0)118 378 7530
[log in to unmask]
http://www.personal.reading.ac.uk/~sxs07itj/index.html



On Thu, May 10, 2012 at 9:35 PM, Dianne Patterson <[log in to unmask]> wrote:
> Bettyann,
> I can't answer your questions, but I love them!
> Absolutely clearheaded and useful to read.
> Thankyou for taking the time to write them.
>
> -Dianne
>
>
> On Thu, May 10, 2012 at 11:51 AM, bettyann <[log in to unmask]> wrote:
>>
>> Aaaand, we're back!  Thanks (in advanced) for your thoughts on Round 1:
>> z-score v beta weight as a measure of functional connectivity
>>
>> Here we are with ...
>> Round 2 for US$500 / 310 GBP / 386 EUR:
>>
>> Assessing change in functional connectivity between pre- and
>> post-conditions using randomise.
>>
>> You may recall from Round 1 that I have a better intuitive feeling for
>> using z-score as a measure of functional connectivity.  I don't yet
>> understand the advantages of using beta weights instead.
>>
>> Now I would like to assess the *change* in functional connectivity between
>> a pre- and post-condition.
>>
>> I have set up a paired t-test design where the lower-level FEAT
>> directories are the results from GLM analysis that produced the functional
>> connectivity maps to my seed region's time course, two per subject (one from
>> the pre-condition; the other from the post-condition).
>>
>> 'Ah,' you ask, 'but what are these input functional connectivity maps?'  I
>> ask the same thing.  Am I correct in thinking that both the cope's (beta
>> weights) and varcope's (variance) will be combined in some statistically
>> sound way to give me a measure of change in functional connectivity (since I
>> am using a repeated measures / paired t-test design where the inputs
>> themselves are functional connectivity maps).
>>
>> The result of this paired t-test produces z-scores, beta weights (copes)
>> and variances (varcopes).  I won't repeat my question from Round 1 here.
>>  No, instead I want to ask about using randomise for inference analysis.
>>
>> I am unsure of how best to use randomise in a repeated measures fashion.
>>  I can deal with the repeated measures part by subtracting pre-condition
>> from post-condition resulting in a difference map, one per subject.
>>
>> Given my current understanding that z-scores reflect correlation, I am
>> leaning toward subtracting z-score (zstat1) volumes to create a
>> zstat-difference, one per subject.  I would then feed these zstat-difference
>> volumes into randomise.  are z-score differences meaningful?  I tell myself
>> the differences are meaningful because these z-scores do reflect
>> correlation.  (But I tell myself a lot of things.)
>>
>> Again I am concerned that I'm not comprehending the strength and beauty of
>> beta weights.  Maybe I should be using the difference in beta weights.  But
>> what about noise ... some of these measurements are noisy, which is
>> uncontrolled (?) in the betas.
>>
>> At this point, I am worried that I've become biased about z-scores.  And
>> that I'm missing something important about beta weights.  Add into the mix
>> the idea of 'difference' and 'change in functional connectivity'.
>>
>> Thoughts?  Comments?
>>
>> Thanks for playing,
>> Thanks for all,
>> * ba
>>
>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> [log in to unmask]
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> (Just East of Harvill)
> 621-9877
> ==============
> "I used to think that the brain was the most wonderful organ in my body.
> Then I realized who was telling me this."
>  - Emo Phillips
> ==============
> If you write me (expecting an answer) and I don't respond within a
> day, then the email may have been lost.
> You can always write me at [log in to unmask]
> ==============
>

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