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These are the files of contrast and matrix design.mat /NumWaves 2 /NumPoints 12 /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 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 design.con /ContrastName1 CTRL>PAT /ContrastName2 PAT>CTRL /NumWaves 2 /NumContrasts 2 /PPheights 1.000000e+00 1.000000e+00 /RequiredEffect 5.042 5.042 /Matrix 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 ________________________________ De: FSL - FMRIB's Software Library <[log in to unmask]> en nombre de Rosalia Dacosta Aguayo <[log in to unmask]> Enviado: lunes, 8 de mayo de 2017 02:03 p. m. Para: [log in to unmask] Asunto: Re: [FSL] group analysis Hi Gabbo, It seems that something went wrong with your design. To see it, we need to see your design.mat and design.com<http://design.com>. Rosalia El 8 may. 2017 20:59, "Gabbo Ramírez García" <[log in to unmask]<mailto:[log in to unmask]>> escribió: The problem is that the image resulting is a image with just a 0.99 value, in fact is a wstrange result for that reason I guess that something is wrong. I want to do Two-Sample Unpaired T-test, because I have a control group and a patients group. for that reason I did used tha command line. I dont know if I am missing some step. RG ________________________________ De: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> en nombre de Blazej Baczkowski <[log in to unmask]<mailto:[log in to unmask]>> Enviado: lunes, 8 de mayo de 2017 01:44 p. m. Para: [log in to unmask]<mailto:[log in to unmask]> Asunto: Re: [FSL] group analysis Hello It is difficult to guess what your problem is based on your description. What type of error do you get? It seems that you want to run a two sample t test. For this you need to specify .grp file -- information on exchangeability, which is missing in your command line. Best, Blazej On 8 May 2017 at 20:11, RGuser <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello FSLuser I am doing seed-analysis for functional resting state images. I get the main signal of some seeds and correlate that signal with the global signal of the brain by Pearson correlation and the resulting image have p- values. I have two groups and now I want to compare the functional maps resulted after correlation signal seed - signal brain. I used this line to do it but it did not work. randomise -i 4dfuntionalmaps -o result -d design.mat -t design.con -m mask.nii.gz -n 500 -T If somebody can help me I will be thankful.