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Hi - no, ignore the FLIRT warnings. The FLAME warnings are of more concern - this almost always means that you have very strong outliers in your data input to FLAME. One thing to check is to load the .gfeat/cope? images into fslview and flick through the timepoints to check for outliers. Cheers, Steve. On Fri, 9 Dec 2005, Cherif Sahyoun wrote: > Hi! > > 2 errors I am getting when running high level analyses in Feat: > - same as in my previous email, everytime flirt is called, I get an error > stating > WARNING: Both reference and input images have an sform matrix set > The output image will use the transformed sform from the reference image > This happens both in low level and high level analyses (more details in my > previous message) > > the reason I am repeating this is it may be related to the following > warnings I get in high level stats: > > WARNING: FLAME stage 2 has given an abnormally large difference to stage 1 > x=50,y=92,z=41 > vox=173818 > zts[0](vox)=7.7325 > zemlowerts[0](vox)=4.62063 > beta_mean[0](vox)=2.73318e-05 > beta_b[0](vox)/beta_c[0](vox)=1.00022e-10 > > WARNING: FLAME stage 2 has given an abnormally large difference to stage 1 > x=50,y=92,z=42 > vox=173819 > zts[0](vox)=7.99212 > zemlowerts[0](vox)=4.7153 > beta_mean[0](vox)=2.73318e-05 > beta_b[0](vox)/beta_c[0](vox)=1.00022e-10 > > I get MANY iterations like these before the analysis finally ends (in > >24hrs!), and am not sure at all what this means or if it's normal... > > any views? > > thx! > cherif > -- Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve