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Thanks so much for your help. One last question, would you use -D with this new design matrix or should it not make any difference? Best Josh On 8 October 2014 21:26, Anderson M. Winkler <[log in to unmask]> wrote: > 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 >> >> Y36 M 12 >> Winterthurerstrasse 190 >> 8057 Zuerich >> >> Tel: +41 44 63 56101 >> email: [log in to unmask] >> http://angelaschoellig.academia.edu/JoshuaBalsters >> > > -- Joshua Henk Balsters Postdoctoral Fellow Neural Control of Movement Lab Department of Health Sciences and Technology ETH Zurich, Switzerland Y36 M 12 Winterthurerstrasse 190 8057 Zuerich Tel: +41 44 63 56101 email: [log in to unmask] http://angelaschoellig.academia.edu/JoshuaBalsters