Hi,
Jolly good - just one minor comment below.
Cheers, Steve.
On 12 Nov 2008, at 21:33, Jerry Yeou-Wei Chen wrote:
> Hello,
>
> I would like to run a simple 2 sample t-test with a nuisance
> variable, and
> also run a linear regression on TBSS data.
> From what I've read in the manuals and the mail list, I think I have
> formulated the correct steps, but I would like to double check in
> particular
> the steps to create the design matrix and contrast files. Hopefully
> others
> can also benefit from having this info all together in one message! (I
> apologize beforehand for the long message! and any lack of clarity!)
>
> After running all the tbss scripts,
> For Simple 2 sample t-test:
> - create design matrix and contrast files using the design_ttest2
> command
>
> For Simple 2 sample t-test w/ 1 nuisance variable:
> - take the files from above and open them with a text editor
> - for the .mat file, add a new column of values under Matrix for your
> nuisance variable (mean-centred)
> - also change NumWaves to 3, and add a value to PPheights for the
> difference
> between the highest and lowest values of your nuisance variable
> - for the .con file, add a 0 to the end of each contrast
> - resulting tstat1 will show areas with higher FA in group 1, tstat2
> shows
> areas higher in group 2
>
> For regression
> - use the same method as above for creating the nuisance variable
> - if you are interested in interactions between group and a
> variable, split
> it to two regressors each containing variable values for one group
> and zeros
> for the other group
Yes - but remember to demean each group's set of values before padding
with zeros.
> - for the .con file, use a 1 to test for positive slopes, -1 to test
> for
> negative slopes, and for interactions use a 1 and -1 for the two
> interaction
> regressors
> - resulting tstats will show areas with FA positively or negatively
> related
> to your regressor (for contrasts simply consisting of 1 or -1) or
> areas
> where one group's FA is related differently to your regressor (for
> contrasts
> with 1 and -1 for interaction regressors)
>
> Please let me know if there are any mistakes with this procedure!
>
> Thanks,
> - Jerry
>
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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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