Steve, You are right on the contrast. However, one needs to make sure they do not interpret the statistics from the contrast. That is to say, you should not interpret the mean pre contrast as regions that are significantly positive/negative from this model. It is fine to use the contrast as a mask for positive versus negative areas with a p-value of .5. The reason you can not interpet the regions as significantly positive/negative is that the statistics for between-subject effects (e.g. mean pre or mean post in this model) is that the error term for the paired t-test is the within-subject error. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Dec 6, 2011 at 4:25 AM, Stephen Smith <[log in to unmask]> wrote: > Hi - - if you expand on how this modelling is working you'll see (e.g. for > two subjects): > > S1pre = PE1 + PE2 > S2pre = PE1 + PE3 > S1post = -PE1 + PE2 > S2post = -PE1 + PE3 > > so if you want MEANpre = (S1pre+S2pre)/2 > > that would be (2*PE1 + PE2 + PE3) / 2 = PE1 + PE2/2 + PE3/2 > > ie a contrast of [1 0.5 0.5] > > I *think* this is right? > > Cheers. > > > > > > On 5 Dec 2011, at 18:53, Lorena Jimenez-Castro wrote: > > Dear FSL experts, > > I have sent you an email last week and I have not received a reply yet, So > I would appreciate any advice you could give me regarding my previous post > (Please see the email below) > > Thank you very much > > Lorena > > > > > > > > > Subject: GLM > > From: Lorena Jimenez-Castro <[log in to unmask]> > > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > > Date: Mon, 28 Nov 2011 22:37:43 +0000 > > Reply > > Dear FSL experts, > > I would like to verify if I am on the right track setting up a design for > a resting state seed based analysis on a group of 13 subjects with pre and > post treatment data. I am trying to set up the design matrix and design > contrast to run the higher-level analysis using FEAT. I know I have to use > “one group paired t test†but also I want to use “contrast masking†> to mask the positive and negative co-activation, that is why I also need to > get from the pre and post groups the correspond negative co-activation mean > and positive co-activation mean. > > I would like to know if the following designs are correct: > > Design matrix: > > subject group EV1 EV2 EV3 EV4 . . . EV13 EV14 > 1 1 1 1 0 0 0 0 > 2 1 1 0 1 0 0 0 > 3 1 1 0 0 1 0 0 > . > . > 13 1 1 0 0 0 0 1 > 14 1 -1 1 0 0 0 0 > 15 1 -1 0 1 0 0 0 > . > . > 26 1 -1 0 0 0 0 1 > > > Design Contrast: > > EV1 EV2 EV3 > EV12 EV13 EV14 > c1: preTx_ positive correlation > post_tx 1 0 0 . . . .. > 0 0 0 > C2:post_tx positive correlation > pre_tx -1 0 0 0 > 0 0 > C3:pre_tx positive correlation mean 1 1 1 1 > 1 1 > C4:post_tx positive correlation mean -1 1 1 1 > 1 1 > C5: pre_tx negative correlation mean 1 -1 -1 -1 > -1 -1 > C6: post_tx negative correlation mean -1 -1 -1 -1 > -1 -1 > C7: preTx_ negative correlation > post_tx -1 0 0 0 > 0 0 > C8: post_tx negative correlation > pre_tx 1 0 0 0 > 0 0 > > > > Contrast masking: > > C1 with C3>0 = real preTx_ positive correlation > post_tx > C2 with C4>0 =real post_tx positive correlation > pre_tx > C7 with C5>0 = real preTx_ negative correlation > post_tx > C8 with C6>0= real post_tx negative correlation > pre_tx > > Am I doing the right thing? > > Any hint on this would be greatly appreciated > > Thanks > > Lorena > > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > > > >