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thanks so much for your help! On 08/15/11, Stamatios Sotiropoulos wrote: > Yes that is fine, the 4th dimension in the input and output files represent different things. Number of DW directions for the input and number of samples from the posterior distribution of the parameters for the merged* files. > > Cheers, > Stam > > On 12 Aug 2011, at 20:57, Ellen Guller wrote: > > > Thanks Stam! So the slices are right on- but I do have a different number of volumes in the bedpost produced merged* files compared to the raw DTI data. Does that matter? > > > > ~Ellen > > > > On 08/12/11, Stamatios Sotiropoulos wrote: > >> Hi Ellen, > >> > >> As long as the output files were produced, you can ignore the messages. > >> > >> Regarding the slices, you may be confusing the number of volumes with the number of slices. The number you mention (5 b0s and 55 directions) is the volumes (the 4th dimension in the dataset). The number of slices is the 3rd dimension. Open the original data file and check how many slices you have. It needs to be 50, i.e. match the number of slices in the bedpostx output. > >> > >> Cheers, > >> Stam > >> > >> > >> > >> ----- Original Message ----- From: "Ellen Guller" <[log in to unmask]> > >> To: <[log in to unmask]> > >> Sent: Friday, August 12, 2011 8:11 PM > >> Subject: [FSL] bedpost output question > >> > >> > >> Hi everyone- > >> I just ran bedpost on 14 subjects and for each subject one of 3 things happened: > >> > >> 1) I got the message "all slices processed" > >> 2) I got the message "For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully." > >> 3) I got the message "Queuing post processing stage" and then the program exited." > >> > >> In all three cases I end up with all the appropriate output files. However, I have 50 slices in the merged* files, although I initially had 60 slices in my data (5 B0's and 55 DWI's). > >> > >> All subjects had the same preprocessing steps (eddy_current correction and field map correction). Any thoughts on what could be going on? Is there a standard line that is printed when bedpost is successful (like in option 1)? > >> > >> Thanks! > >> > >> ~Ellen > > > > -- > > University of Wisconsin, Madison > > Neuroscience Training Program > > Ph.D. Dissertator > > [log in to unmask] > > (608) 263-3689 > > -- University of Wisconsin, Madison Neuroscience Training Program Ph.D. Dissertator [log in to unmask] (608) 263-3689