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Hi Michael Unless you use the --lrtarget3 option, the output fdt_matrix3.dot is a symmetric matrix, and therefore only the upper half is stored. You should symmetrise it before you run my matlab code (M=M+M’); It is not surprising that it is spare. You probably need to increase the number of samples. Saad On 31 Jan 2014, at 00:48, Michael <[log in to unmask]<mailto:[log in to unmask]>> wrote: Many thanks Saad, this now works with the code you gave me in Matlab. Unfortunately the connectivity matrix is almost empty except for a few entries, all in the upper right part. Would you know why that would happen? I sent you the files by email if that could help. -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>