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Hi - yes, the IRTK nonlinear registration programs are not working, as you don't have the necessary system libraries installed (see previous posts on this). Most operating systems do come with the necessary libraries - exactly what OS are you running? You should see these error messages just by typing: $FSLDIR/bin/DR/nreg which, if it is happy with the libraries, should just print out Usage information. Cheers, Steve. On 3 Dec 2007, at 20:19, James Andrews wrote: > Hi Steve, > > The slicedir output looked fine to me. There are numerous error > messages in the *.e* files, which I don't know how to interpret. I > uploaded the whole directory like you suggested, so that you can > take a look and see what's going on. > > The upload ID :597106 > > As a backup, I also emailed the data to [log in to unmask] using www.yousendit.com > . The file is called "fsldata.zip". > > Thanks so much, > James > > On Dec 3, 2007 1:07 AM, Steve Smith < [log in to unmask]> wrote: > Hi - did the slicesdir output created by tbss_1 look fine? > > Are there any informative messages in any *.o* or *.e* files in FAi or > one level up? If it's still not clear, then please upload the whole > directory (one level up from FAi) and we can take a quick look. > > Please upload the files in a single compressed tarfile to > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > And then email me the upload ID. > > Cheers. > > > On 2 Dec 2007, at 21:37, James Andrews wrote: > > > Hi, > > > > I used the "top" command and I am sure now that tbss_2_reg -T does > > run briefly, produces the files I mentioned, and then stops. And I > > haven't done anything to set the SGE_ROOT environment variable. > > I'm at a real loss for how to get tbss_2_reg -T to run correctly. > > Do you have any suggestions? I've tried to run it several times now > > but it just does this every time. > > > > Many thanks, > > James > > > > On Dec 2, 2007 3:01 AM, Steve Smith < [log in to unmask]> wrote: > > Hi, > > > > By default FSL doesn't use SGE - so as long as you haven't somehow > got > > the SGE_ROOT environment variable set, it shouldn't be looking for > it. > > > > Hence - it should print out what you saw, and then start running all > > the registrations. Are you sure it wasn't running? Try deleting FAi/ > > *.msf and try again? Once it's running, try typing "top" in a > separate > > terminal to check if anything is running. > > > > Cheers. > > > > > > On 1 Dec 2007, at 22:56, James Andrews wrote: > > > > > Hi Steve, > > > > > > I would like to simply run "tbss_2_reg -T" on our single linux > > > machine. How do I fix it > > > so that the script does not try to run with SGE? > > > > > > Many thanks, > > > James > > > > > > > > > On Dec 1, 2007 2:16 AM, Steve Smith < [log in to unmask] > > wrote: > > > Hi, > > > > > > It looks like the script thinks that you are running SGE, and that > > it > > > has submitted all the jobs to your cluster? > > > > > > Cheers. > > > > > > > > > > > > On 1 Dec 2007, at 00:47, James Andrews wrote: > > > > > > > Hi, > > > > > > > > I have run "tbss_1_preproc" without any problems, but when I run > > > > "tbss_2_reg > > > > -T" (which I thought should take several hours if I have 13 > > > > subjects) it > > > > *instantaneously* gives me the message below. Also, for each > > > > subject it > > > > outputs one .msf file and another file (eg. > > "tbss_2_reg.e12436.1"). > > > > All > > > > these files, though, contain 0 bytes. I would greatly > appreciate > > > > guidance > > > > if anyone recognizes what is going wrong. > > > > > > > > Many thanks, > > > > James Andrews > > > > Stanford University > > > > > > > > CON_0659_dti_FA_FAi_to_target > > > > CON_1906_dti_FA_FAi_to_target > > > > CON_2552_dti_FA_FAi_to_target > > > > CON_3204_dti_FA_FAi_to_target > > > > CON_4606_dti_FA_FAi_to_target > > > > PREM_0125_dti_FA_FAi_to_target > > > > PREM_1355_dti_FA_FAi_to_target > > > > PREM_3501_dti_FA_FAi_to_target > > > > PREM_4208_dti_FA_FAi_to_target > > > > PREM_4456_dti_FA_FAi_to_target > > > > PREM_4751_dti_FA_FAi_to_target > > > > PREM_5352_dti_FA_FAi_to_target > > > > PREM_5901_dti_FA_FAi_to_target > > > > 12436 > > > > > > > > > > > > --------------------------------------------------------------------------- > > > Stephen M. Smith, Professor of Biomedical Engineering > > > Associate Director, Oxford University FMRIB Centre > > > > > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > > > +44 (0) 1865 222726 (fax 222717) > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > > > > --------------------------------------------------------------------------- > > > > > > > > > > --------------------------------------------------------------------------- > > Stephen M. Smith, Professor of Biomedical Engineering > > Associate Director, Oxford University FMRIB Centre > > > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > > +44 (0) 1865 222726 (fax 222717) > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > --------------------------------------------------------------------------- > > > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------