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Thank you very much Stam. You're right, my brain mask did have values other than exact 0s and 1s. I had resampled the mask so ended up with 0.3's and 0.7's etc... Thanks a lot. Shaza On Thu, Oct 28, 2010 at 1:32 PM, Stamatios Sotiropoulos <[log in to unmask] > wrote: > Hi, > > I would rerun BET and make sure that the brain mask has no funny values > (you can check that using fslmaths). > > Cheers, > Stam > > On 28 Oct 2010, at 16:51, shaza zaghlool wrote: > > Yes I ran that before I ran bedpostx. There were no problems detected. > > > On Thu, Oct 28, 2010 at 11:50 AM, Stamatios Sotiropoulos < > [log in to unmask]> wrote: > >> 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 >>> >> >> >> > >