Thanks again for the reply Steve.
However, I could use some more clarification of two points:
1) For the .con file, does PPHeights refer to the range of values for each
column of contrast matrices, or the design matrices (like PPheights in the
.mat file)?
2) For the .con file again, does the number of contrasts factor into the
statistics at all? (e.g. for correction for multiple comparisons) or does
the "randomise" function just use it to know how many lines to read?
Thanks for your time,
- Jerry
On Thu, 13 Nov 2008 08:29:26 +0000, Steve Smith <[log in to unmask]> wrote:
>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
>>
>
>
>---------------------------------------------------------------------------
>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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