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Can you check the dimensions of every file, just to be positive? Are you using the same exact procedure for every subject? Where are you getting the cortical thickness data from? Maybe it's the surface measurements --> volume measurements that is causing the problem. On 01/23/2014 10:52 AM, Nadejda Zaharieva wrote: > Hello, > > I have a few questions regarding using SPM for structural MRI. > > I have two groups (N=5): control and disease. The brains are > pre-processed and in register with each other, and have the same > dimensions and orientation. Cortical thickness surface measurements > were calculated and these values stored as intensities in3D NIfti > imagesin the same space as the registered brains. All that is left to > do is to run a t-test for each voxel locationin the thickness data. > > I have tried using thet-test in the Second-Level Analysis underfMRI > statistics for this purpose but it doesn't seem to work. Specifically, > it says "Inner matrix dimensions must agree"in the Matlab consoleand > I'm pretty confident the images are the same dimensions. > > I am going to "Specify 2nd Level" and entering my groups. Then, I > click "Estimate" and select the "SPM.mat" file. Is there something > else I should be doing instead? > > Thank you for your time, > > > Nadejda Zaharieva > Candidate for M.Sc. Neuroscience; in progress > B.Sc. Hons Computational Science, Chemistry