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Hi Nic > Dear Experts, > > I am relatively new to FSL but I am enjoying working with the program.I have run bedpost analysis on my DTI data which consists of two groups of subjects.I now want to compare connectivity between a thalamus seed mask and some cortical structure masks in my two groups. From tutorials, documentation and this list I have got to the point were I have performed both a parcellation and a seed-target analysis so I have both fdt_path files for seeds to my desired structures, as well as seed_to_target files for each subject. I defined my masks in standard space and used a linear transform to diffusion space for analysis. I have a couple of questions: > > If I wish to compare connectivity between the thalamus and a cortical mask what method is better, parcellation targets, i.e seed_target output or FDT_paths output. > > I am inclined to prefer the parcellation data as I have read on this list that I can divide the number of streamlines reaching each target from the seed by the waytotal to give me a connectivity value (exactly what I am looking for as I hope I can then export these to compare the groups statistically), does this sound appropriate or have I misinterpreted? Yes that's fine. > > Finaly, I am concerned that my waytotals are always the same across subjects, I assume this is due to using a linear transform from standard space masks but I am worried that I have made an error, is it ok that my waytotal always comes out identically and if this is the case is their really any need to do the division prior to stats as values will already be normalised? The waytotal will be the same if you use the same seed mask, and no inclusion or exclusion masks, which is probably the case for you. Cheers Saad > > Thanks for any advice and apologies for rambling post > > best > > Nic > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad