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Hi, On 28 Feb 2008, at 15:18, Shireen, Kwiatkowska wrote: > Dear Fsl Users, > > I have a randomise question concerning siena results. > > I have 2 groups: > > - young (n= 24) > - old (n=23), > > both scanned at 2 time points. > > I'm interested in differences in brain volume changes between these > two groups. > > I have run siena and flow2std on all of my subjects, and performed > randomise on the flow_all_subjects.nii.gz as follows: > > randomise -i flow_all_subjects.nii.gz -o TwoSampT -d matrix47.mat -t > matrix47.con -m avg152T1_brain.nii.gz If you've run siena_flow2std then the mask image should be the brain edge mask: $FSLDIR/data/standard/MNI152_T1_2mm_edges Unless you change the siena_flow2std script then this should definitely be the mask image used for the -m option in randomise. > 1. the first question I have: may I use avg152T1_brain.nii.gz > instead of producing my own mask, and if not, how do I produce a > mask. Is this equal with constructing a template for VBM analysis? > > 2. I have created the design matrix using the GLM_Gui, and am not > sure if it's exactly the matrix I need. > > matrix47.con: > > /ContrastName1 group A > group B > /ContrastName2 group B > group A > /ContrastName3 group A mean > /ContrastName4 group B mean > /NumWaves 2 > /NumContrasts 4 > /PPheights 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > /RequiredEffect 1.211 1.211 0.847 0.866 > > /Matrix > 1.000000e+00 -1.000000e+00 > -1.000000e+00 1.000000e+00 > 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 > > > matrix47.mat: > > /NumWaves 2 > /NumPoints 47 > /PPheights 1.000000e+00 1.000000e+00 > > /Matrix > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > 0.000000e+00 1.000000e+00 > > > 3. randomise gave me 3 types of output files, and I understand the > basic meaning of those results, I only cannot figure out, which file > goes with which specific question. > > I have > TwoSampT_max_tstat1.nii.gz > TwoSampT_max_tstat2.nii.gz > TwoSampT_max_tstat3.nii.gz > TwoSampT_max_tstat4.nii.gz > > TwoSampT_tstat1.nii.gz > TwoSampT_tstat2.nii.gz > TwoSampT_tstat3.nii.gz > TwoSampT_tstat4.nii.gz > > and > > TwoSampT_vox_tstat1.nii.gz > TwoSampT_vox_tstat2.nii.gz > TwoSampT_vox_tstat3.nii.gz > TwoSampT_vox_tstat4.nii.gz For the different numbers 1-4, see your contrasts file - the ContrastName lines should make this clear hopefully. Cheers, Steve. > > > > Looking forward to some answers, as I'm a bit lost... > > Greetings, > > Shireen Kwiatkowska > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------