Hi Joshua,

1) Yes, you can just drop the "-e design.grp" and all subjects will automatically fall into the same group.

2) The design is fine, but the contrast would be different and less intuitive. Instead, a suggestion is:

EV1: Code as +1 or -1 for each group, and mean-center if the number of subjects isn't the same on each;

EV2-EV9: code as 0 or 1 for each centre (no need to omit any centre; the design won't be rank-deficient this time);

EV10-EV12: use for age, FIQ and FD, mean centered.

The contrasts are then:

C1 (A>B): 1 0 0 0 0 0 0 0 0 0 0 0
C2 (A<B): -1 0 0 0 0 0 0 0 0 0 0 0

C3 (global mean): 0 1/8 1/8 1/8 1/8 1/8 1/8 1/8 1/8 0 0 0

C4 (mean A): 1/2 1/8 1/8 1/8 1/8 1/8 1/8 1/8 1/8 0 0 0
C5 (mean B): -1/2 1/8 1/8 1/8 1/8 1/8 1/8 1/8 1/8 0 0 0

3) sure!

All the best,

Anderson

On 8 October 2014 18:14, Joshua Balsters <[log in to unmask]> wrote:

Hi Anderson

Thank you so much for your quick reply. 

1) If I don't use the -e flag then will it automatically permute across all subjects or do I need to change the .grp file to all 1's?

2) I've attached an image of the design matrix but I can give you the exact variables if you'd prefer. I've modelled all the centres except 1 so the overall mean isn't modelled. This was to avoid the message for rank deficiency of the model.

3) thanks for this! I'll use these as well. 

Best

Josh

On 8 October 2014 18:30, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Josh,

For (1): In the group indicator, use all ones. This column in randomise is related to exchangeability groups, and here you want all subjects (all!) in the same group.

For (2): It sounds the overall mean is modelled across the regressors for the scan centres, so demeaning shouldn't be necessary. But to be sure, please, include your design in the email.

For (3): There are extra flags: --vxl and --vxf, one to specify the 4D file, the other with the position they occupy in the design matrix.

Hope this helps!

All the best,

Anderson

On 8 October 2014 15:32, Joshua Balsters <[log in to unmask]> wrote:

Hi

I wanted to check a couple things about my use of Randomise...

My design matrix is a two sample t-test with covariates of no interest (8 categorial regressors for different scan centres and 3 continuous regressors which I've demeaned before entering them into the design matrix). The inputs are Z-transformed resting state data.

1) I get an error saying "Design matrix uses different groups (for different variances), but these do not contain separable EVs for the different groups... Ignore if you're intending to use the groups file to define exchangeability blocks for randomise". If I understand correctly this is for repeated measures rather than comparing two independent groups. Should I ignore this message?

2) as I don't model a constant should I be using the -D flag as well?

3) for a voxel-wise regressor like grey matter volume, is it enough to specify the file when setting up the design matrix or are then any extra flags I need to use when running randomise?

Thanks for your help!
Josh

--
Joshua Henk Balsters
Postdoctoral Fellow

Neural Control of Movement Lab
Department of Health Sciences and Technology
ETH Zurich, Switzerland

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Tel: +41 44 63 56101
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http://angelaschoellig.academia.edu/JoshuaBalsters