Hi Anderson,
Thanks for your reply. If I have only 1 column in the design.mat for
group, how would this look for the contrast? I've attached my old
design.con and .mat files (patient vs. control, covariate for age and
sex, but not controlling for centre), and my guess as to what the new
design.con and .mat files would look like, additionally controlling for
centre. Please let me know if these look correct.
Thanks again,
Colleen
---
Colleen Rollins, PhD Candidate
Department of Psychiatry
University of Cambridge
Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ
On 2018-04-08 20:45, Anderson M. Winkler wrote:
> Hi Colleen,
>
> You can code centre as you indicated (with 6 EVs for 6 centres, each
> coded as 1 or 0). But in that case, remove your current EV1 and EV2
> and replace them for a single EV that is +1 or -1 for patients and
> controls, otherwise the design becomes rank deficient. You need to
> change your contrasts accordingly then.
>
> All the best,
>
> Anderson
>
> On 6 April 2018 at 06:55, Colleen Rollins <[log in to unmask]> wrote:
>
>> Dear FSL Developers,
>>
>> I'd like to do a standard VBM analysis (patients vs. controls,
>> covaried for age and sex) on data from a multi-centre study and I'm
>> wondering how I should construct my design matrix to code centre as
>> a dummy variable. Currently, my design matrix looks something like
>> this (group (patients vs. control) in the first 2 columns, then age
>> and sex (both demeaned).
>> /NumWaves 4
>> /NumPoints 183
>> /PPheights 1 1
>> /Matrix
>> 1 0 6.360655738 0.278688525
>> 1 0 -5.639344262 -0.721311475
>> 0 1 -4.639344262 -0.721311475
>> 0 1 9.360655738 0.278688525
>> ...
>> To include centre as dummy variable, would I add a column for each
>> centre and enter either a 1 or a 0 depending on whether that scan is
>> from that centre? For instance, there were 6 centres (scans for
>> patients and controls collected at each) in the study, so centre as
>> a dummy variable might look something like this?
>> 0 0 1 0 0 0
>> 0 0 0 1 0 0
>> 1 0 0 0 0 0
>> Moreover, would this be the best way to control for centre?
>>
>> Many thanks,
>> Colleen
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