 |
 |
Hi, On 18 Feb 2009, at 00:42, Michael Scheel wrote: > Hi Steve, > > the design matrix was an example for a paired t-test of 5 people (to > make the matrix shorter - i changed the matrix, but stick to the > example with 5 and hope now it makes more sense and that is indeed > the correct design.matrix). > And yes - the answer to the previous FLAME contrast-of-contrast > question did clarify the situation a bit. However, maybe let me try > to rephrase: > > I assume that negative numbers in the output from siena > (A_to_B_flow.nii.gz) mean that there has been atrophy in this > region, while positive mean that growth occured. > >siena_flow2std A B< just transforms these into standard space (and > keeps the meaning of negative numbers being atrophy and positive > being growth). correct > Now if I test for differences between the drug and the placebo > condition with this design matrix and contrasts. > > Input Group EV1 EV2 EV3 EV4 EV5 EV6 > s1_prepost_drug 1 1 1 0 0 0 0 > s2_prepost_drug 1 1 0 1 0 0 0 > s3_prepost_drug 1 1 0 0 1 0 0 > s4_prepost_drug 1 1 0 0 0 1 0 > s5_prepost_drug 1 1 0 0 0 0 1 > s1_prepost_plac 1 -1 1 0 0 0 0 > s2_prepost_plac 1 -1 0 1 0 0 0 > s3_prepost_plac 1 -1 0 0 1 0 0 > s4_prepost_plac 1 -1 0 0 0 1 0 > s5_prepost_plac 1 -1 0 0 0 0 1 > > Contrasts > EV1 EV2 EV3 EV4 EV5 EV6 > Condition A>B 1 0 0 0 0 0 > Condition B>A -1 0 0 0 0 0 > > So my understanding is that Contrast_1 (Condition A>B) is asking for > where has more growth (or less atrophy) happened during the drug > condition compared to placebo? > And Contrast_2 (Condition B>A) is asking the same thing for the > placebo condition compared to the drug condition? > > Is my interpretation right? Thanks a lot, Michael That's right - and you can look at the separate pre- or post- group mean effects (though not using this model!) to help disambiguate what those contrasts are saying. Cheers. > > > On 17-Feb-09, at 12:50 AM, Steve Smith wrote: > >> Hi, >> >> It's not clear how your design relates to your "20" drug/placebo >> timepoints - however maybe this is answered by my previous email, >> about FMRI contrasts-of-contrasts? >> >> Cheers. >> >> >> On 17 Feb 2009, at 00:27, Michael Scheel wrote: >> >>> Dear fsl experts, >>> >>> I have a question regarding the output of siena. We scanned 20 >>> subjects at four different timepoints - 1) PreDrug 2) PostDrug >>> 3)PrePlacebo 4) PostPlacebo. >>> I used siena to estimate atrophy/growth in both conditions (Placebo >>> and Drug) individually >>> >>>> siena subject_predrug.nii.gz subject_postdrug.nii.gz >>>> siena subject_preplacebo.nii.gz subject_postplacebo.nii.gz >>> >>> As suggested on the website I then did >run siena_flow2std A B< and >>> used fslmerge to merge all the A_to_B_flow_to_std.nii.gz into one 4D >>> file (all_flow_to_std.nii.gz) so that first all the 20 were flow >>> images between Pre and Post for the DrugCondition and the last 20 >>> were the changes under the Placebo Condition. I then set up matrix >>> and contrasts with the Glm_gui wizard to set up a paired ttest and >>> used randomise with the threshold-free-enhancement-option. >>> >>> As the whole procedure was rather to control that there wasn't any >>> particular atrophy so I didn't expect any significant results. >>> However I do get signifant voxels for the Contrast 'Condition B > >>> Condition A' Contrast and was wondering how to interpret these >>> findings, would it mean that the atrophy is bigger in the Placebo >>> Condition? >>> >>> Below my design matrix and contrast (example for 5 subjects) >>> >>> Input Group EV1 EV2 EV3 EV4 EV5 EV6 >>> 1 1 1 1 0 0 0 0 >>> 2 1 1 0 1 0 0 0 >>> 3 1 1 0 0 1 0 0 >>> 4 1 1 0 0 0 1 0 >>> 5 1 1 0 0 0 0 1 >>> 6 1 -1 1 0 0 0 0 >>> 7 1 -1 0 1 0 0 0 >>> 8 1 -1 0 0 1 0 0 >>> 9 1 -1 0 0 0 1 0 >>> 10 1 -1 0 0 0 0 1 >>> >>> Contrasts >>> EV1 EV2 EV3 EV4 EV5 EV6 >>> Condition A>B 1 0 0 0 0 0 >>> Condition B>A -1 0 0 0 0 0 >>> >>> >>> Thanks, Michael >>> >> >> >> --------------------------------------------------------------------------- >> 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 >> --------------------------------------------------------------------------- > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------