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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 ---------------------------------------------------------------------------