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Hi Saad, Many thanks! Also I would like to point out that when I ran tbss_2_reg -T in 4.1.4 there is an error. It was failing to get to -T, but was fine for -n. We moved the /bin/rm -f FA/.commands somewhere else and it appears to works now. [ "$1" = "" ] && Usage echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog /bin/rm -f FA/.commands if [ $1 = -n ] ; then Cheers, Vanessa -- Vanessa Lim (PhD) Psychology Department University of Auckland Private Bag 92019 Auckland, New Zealand On 8/12/09 11:28 AM, "Saad Jbabdi" <[log in to unmask]> wrote: > Hi Vanessa, > > You need to create your own transform files for your own data. > > You can use the GUI for that. Please read the appropriate section in > the doc: www.fmrib.ox.ac.uk/fsl/fdt/fdt_reg.html > > Cheers, > Saad. > > On 12 Aug 2009, at 13:17, Vanessa Lim wrote: > >> Hi, >> >> Earlier I posted that I didn't get any files using 4.1.4 from my >> error: >> "Queuing post processing stage" with Terminal error but I was wrong >> I did get bedpostX >> directory with what look have the same file names as the tutorial, >> although I have a few >> extra (commands.txt, logs folder, monitor). >> >> When I went to run "vecreg -i dyads1 -o dyads1_to_standard -r >> $FSLDIR/data/standard/MNI152_T1_2mm -t xfms/diff2standard.mat" >> >> I couldn't because in my xfms folder I only have an eye.mat and no >> others (i.e. in the >> tutorial folder there is also diff2standard.mat, diff2str, >> standard2diff, standard2str etc). >> >> Can I just copy the files from the tutorial xfms folder or is the >> bedpostx supposed to >> generate these for each individual subject? >> >> I've run 4 dti sessions and all 4 only have xmfs with eye.mat. 2 of >> the 4 had the >> "queuing post processing stage" then Done! and 2 didn't. >> >> Regards, >> Vanessa >> > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > +44 (0) 1865 222523 (fax 717) > www.fmrib.ox.ac.uk/~saad