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Could you please run bedpostx_datacheck on the directory that contains the data, bvals, bvecs...? Are there any problems identified? Stam On 28 Oct 2010, at 16:26, shaza zaghlool wrote: > Yes the brain mask covers the whole brain. I still don't know what the problem is.. > Thanks, > > On Thu, Oct 28, 2010 at 11:16 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote: > Hi, > > bedpostx should process all slices and you should be able to see the results in fslview. Could you check the brain mask and make sure that this covers the whole brain volume? > > Cheers, > Stam > > > On 28 Oct 2010, at 16:01, shaza zaghlool wrote: > > > Hello, > > I have a question regarding bedpostx. When I ran it on my dataset with the default parameters, it finished in about 4 hours. It kept showing the number of slices being processed and it only reached 16 slices when i actually have a lot more than 16. Also, when I visually checked what merged_f1samples.nii.gz, merged_f2samples.nii.gz, merged_ph1samples.nii.gz,... etc, in FSLView, they appeared to be only the top quarter of the brain and the rest was cut out. Is that normal? > > Also, I used this output of bedpostx as input to probtrackx and I was specifying a seed and target, but the program never converges and seems to go on forever. How long should it take for probtrackx to run and what can cause it to not converge? > > Thanks >