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Hi, On 22 Jan 2009, at 15:38, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > > Hi FSL experts, > > I just run "randomise" and met some problems. > > My study design: > Four subjects' groups, control, disease1, disease2, disease1+2. > I want to get the main effect of disease1, disease2 and interaction. > I made the design files with Glm program. > The details: > number of EVs: 4 > Group: 1 1 1 1 1 1 1 1 > EV1: -1 -1 -1 -1 1 1 1 1 > EV2: -1 -1 1 1 -1 -1 1 1 > EV3: 1 1 -1 -1 -1 -1 1 1 > EV4: 1 1 1 1 1 1 1 1 > Contrasts:3 F-tests:3 > C1: 1 0 0 0 > C2: 0 1 0 0 > C3: 0 0 1 0 > F1: 1 0 0 > F2: 0 1 0 > F3: 0 0 1 > > The script I run: > randomise -i all_FA_skeletonised -o sde_FA3.4_skeletonised -m > mean_FA_skeleton_mask -d design.mat -t design.con -f design.fts -g > design.grp -n 10000 -c 3.4 -V > This result I got: > sde_FA3.4_skeletonised_fstat1.nii.gz > sde_FA3.4_skeletonised_fstat2.nii.gz > sde_FA3.4_skeletonised_fstat3.nii.gz > sde_FA3.4_skeletonised_tstat1.nii.gz > sde_FA3.4_skeletonised_tstat2.nii.gz > sde_FA3.4_skeletonised_tstat3.nii.gz > sde_FA3.4_skeletonised_maxc_tstat1.nii.gz > sde_FA3.4_skeletonised_maxc_tstat2.nii.gz > sde_FA3.4_skeletonised_maxc_tstat3.nii.gz > sde_FA3.4_skeletonised_max_fstat1.nii.gz > sde_FA3.4_skeletonised_max_fstat2.nii.gz > sde_FA3.4_skeletonised_max_fstat3.nii.gz > sde_FA3.4_skeletonised_max_tstat1.nii.gz > sde_FA3.4_skeletonised_max_tstat2.nii.gz > sde_FA3.4_skeletonised_max_tstat3.nii.gz > sde_FA3.4_skeletonised_vox_fstat1.nii.gz > sde_FA3.4_skeletonised_vox_fstat2.nii.gz > sde_FA3.4_skeletonised_vox_fstat3.nii.gz > sde_FA3.4_skeletonised_vox_tstat1.nii.gz > sde_FA3.4_skeletonised_vox_tstat2.nii.gz > sde_FA3.4_skeletonised_vox_tstat3.nii.gz > According with my understand, "1" is desease1's main effect, "2" is > desease2's main effect and "3" is the interaction. > > Is it correct? > > When I check the result in "_vox_fstat" files, there still some data > lower than 0. Is it correct? In my idea, the F-test should be all > positive. > Indeed - that is slightly concerning - can you upload the data to Matthew to look into please? > The third quesiton: why there is no "maxc_fstat" files? > Becuase you didn't specify the -F option (see randomise usage output). > The last question: I found there are several text files built at the > same time (e.g., sde_FA3.4_skeletonised_max_fstat1.txt). What is > means of them? I did not find any manual in the website. > There is a randomise manual http://fsl.fmrib.ox.ac.uk/fsl/randomise/ but it doesn't mention the text files. matthew, what's in that file? Cheers, Steve. > > Thank you very much! > > Xiaochu Zhang PhD > > Visiting Research Fellow > > Neuroimaging Research Branch > > National Institute on Drug Abuse - IRP > > Biomedical Research Center > > 251 Bayview Blvd. > > Suite 200 (NIDA) > > Baltimore MD > > 21224 > > Tel: 443-740-2619 > > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------