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Hi Steve - Now I am getting the output after setting -n 20. Most likely the problem was that the job got mistakenly killed? Thanks for your help. Best, Miguel On Mon, Aug 17, 2009 at 11:21 PM, Steve Smith <[log in to unmask]> wrote: > Hi - try adding "-n 20" to limit the number of permutations whilst you are > sorting this out. Does it appear to go through the permutations and claim > to save any output? Are you sure you looked for output in > /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/ ? > > Cheers. > > > > > On 18 Aug 2009, at 00:03, Miguel Burgaleta wrote: > > Thanks Steve -- Hm, I do have permissions in that folder, but got no >> output nor error message. >> Do you see something weird in the command?: >> >> ***************** quoting ************************* >> randomise -i /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/FA_4D.nii.gz >> -o /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/TvalFA_ -d >> /ifs/four_d/MIGUEL/FULL_SAMPLE/STATS/DesignMatrices/randomise/DM_randomise_IQ_speed.mat >> -t >> /ifs/four_d/MIGUEL/FULL_SAMPLE/STATS/DesignMatrices/randomise/Contrast.con >> -m /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/mask_WM_4stats.img -T >> >> ****************************************************** >> >> Miguel >> >> >> >> >> >> On Mon, Aug 17, 2009 at 9:27 AM, Steve Smith <[log in to unmask]> >> wrote: >> Hi - the randomise output is determined by the output filename you give it >> - after "-o" on the command - if you don't specify a directory name as part >> of this option the output will be in the directory you run randomise is. If >> this directory is not writable by you I suppose there may be no output. >> >> Cheers. >> >> >> >> On 17 Aug 2009, at 18:22, Miguel Burgaleta wrote: >> >> Thanks Steve! >> I was somehow expecting the /Custom line to specify the path for the >> output... If not, where should I look at? randomise seems to run ok but I am >> unable to find the output! >> >> Best, >> Miguel >> >> On Mon, Aug 17, 2009 at 2:54 AM, Steve Smith <[log in to unmask]> >> wrote: >> HI, Custom is for historical reasons - not used generally now. >> >> PPheight is best left in, as it may be used by some programs - it should >> be the peak-peak height of each regressor. >> >> Cheers. >> >> >> >> On 14 Aug 2009, at 21:34, Miguel Burgaleta wrote: >> >> Hello, >> >> I am trying to set up the design.mat file in order to run randomise. >> However, I have 2 >> questions about the meaning of some of the lines in the file and I was >> unable to find an >> answer by browsing your archives. >> >> 1. What does the /Custom line means? >> 2. Is it true that I can just remove the /PPheight line? >> >> Thanks in advance for your time! >> >> Cheers, >> Miguel >> >> >> >> >> --------------------------------------------------------------------------- >> 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 > --------------------------------------------------------------------------- >