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Hi - no - the input data is the 4d timeseries data and the output a (masked) corrcoef map. -------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford. OX3 9 DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------- On 7 Nov 2012, at 18:19, Jamy Andy <[log in to unmask]> wrote: > Thanks Steve for this, > Just to make sure I am doing this right. My input will be the result of my functional connectivity analysis, e.g. "thresh_zstat1", my design will be my time course seed ROI "BSC_ROI.txt", and then I want to add a mask to look at the correlation coefficient between my seed ROI and the area within the mask? and of course as you suggested the option --des_norm and --dat_norm and --demean. > > so it will look like: > fsl_glm -i thresh_zstat1 -d BSC_ROI.txt -o toto -m mask.nii.gz --des_norm --dat_norm --demean > > I guess that the output will be a text file with coefficient correlation.. between my seed ROI and the area included in the mask? > Thanks > J. >