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Hi, I'm afraid that the only documentation at the moment is: fslcc - run cross-correlations between every volume in one 4D data set with every volume in another (for investigating similarities in ICA outputs). and Usage: fslcc [-noabs] <first_input> <second_input> [cc_thresh] -noabs: Don't return absolute values (keep sign). However, it is really a very easy tool and if you give it two 4D datasets then it will calculate the cross-correlation between all pairs of 3D images from the two datasets. It displays the output in three columns: volume number from the 1st 4D dataset volume number from the 2nd 4D dataset correlation value Also note that the volume numbers start at 1, not 0, for this tool. Hope this helps. All the best, Mark On 15 Jun 2010, at 08:11, Mohamed Bahri wrote: > Dear FSL experts, > > Are there any detailed documentations about fsl commands line > (especially for fslcc)? > > Many thanks, > > Mohamed >