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Thanks, Steve. I can’t find the old data upload URL, so here’s a Dropbox link to a FIX_debugging.tar.gz file containing all of the output and error files from my latest FIX training attempt. https://www.dropbox.com/s/h1o6uuvni72anvr/FIX_debugging.tar.gz I’ve copied individual features (from the subject.feat/fix folder) to the “training_features” subfolder. Thanks for taking the time to look at this. Cheers, David On Nov 8, 2014, at 4:21 AM, Stephen Smith <[log in to unmask]> wrote: > Hi David - it's hard to tell from this what's going wrong with the training-weights creation. If you want to create a tarfile containing all of the output folders/files being created we can take a look. > > Regards, Steve. > > > On 7 Nov 2014, at 19:42, David V. Smith <[log in to unmask]> wrote: > >> Hi Steve, >> >> My mistake — I wasn’t actually using the compiled files (I didn’t change the default). FSL_FIX_MATLAB_MODE=1 >> >> Unfortunately, I don’t have SGE set up here; I’m not sure that option is set up by default (it doesn’t seem to be). >> >> I tried FIX with the Standard.RData training weight files, and it worked fine (as did the subsequent cleaning step). So, it looks like I’m mainly having trouble generating a study-specific <training>.RData file. Any ideas? >> >> Thanks for your help. This is really cool software, and I’m excited to use it! >> >> Cheers, >> David >> >> >> >> On Nov 7, 2014, at 2:23 AM, Stephen Smith <[log in to unmask]> wrote: >> >>> Hi - I would not necessarily recommend that you recompile the matlab - that shouldn't be necessary? >>> >>> The LOO option will use SGE if it's setup - so you may want to check on that - and also try running a single FIX run with a presupplied training-weights file to see if that runs OK. >>> >>> Cheers. >>> >>> >>> >>> On 6 Nov 2014, at 21:28, David V. Smith <[log in to unmask]> wrote: >>> >>>> Hi, >>>> >>>> I’m also having trouble setting up FIX. Our sysadmin has compiled the Matlab binaries and has changed the paths in the settings.sh file (described in the README file). >>>> >>>> When I train the classifier on my hand labels without the LOO, there’s no training.Rdata output file. And when I use the LOO option during training, it produces the errors below and dumps several files with strange names (e.g., "302:.e6151" and "302:.o6151”): >>>> >>>> leaving-out: /mnt/delgadolab/disk02/labdata02/AffInf01/FSL/203/run1.feat >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> /bin/sh: 1: 302:: not found >>>> >>>> I’m not sure how to debug from here. It looks like our environment is set up correctly when I source the settings.sh file. The only other I error I see is in one of the matlab logs: >>>> >>>> tail: cannot open `/mnt/delgadolab/disk02/labdata02/AffInf01/FSL/203/run1.feat/fix4melview_training3_LOO_thr1.txt' for reading: No such file or directory >>>> >>>> But I’m assuming that file didn’t get created because something broke earlier… >>>> >>>> Thanks for any help! >>>> >>>> Cheers, >>>> David >>>> >>>> >>>> >>>> On Nov 2, 2014, at 7:26 AM, Alireza Sedghi <[log in to unmask]> wrote: >>>> >>>>> Dear FSL experts >>>>> i want to install FIX on my ubuntu 14.04 , i have downloaded it and unpacked it to my home directory , the setting.sh is somehow confusing ! i have MATLAB installed already , which part of setting.sh must change ? >>>>> how can i change the matlab startup option >>>>> i really appreciate if you can help >>>>> >>>> >>>> ---------------------------------------------- >>>> David V. Smith, Ph.D. >>>> Postdoctoral Fellow, Delgado Lab >>>> Department of Psychology >>>> Rutgers University >>>> Newark, NJ 07102 >>>> ---------------------------------------------- >>> >>> >>> --------------------------------------------------------------------------- >>> 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 >>> --------------------------------------------------------------------------- >>> >>> Stop the cultural destruction of Tibet >>> >>> >>> >>> >> >> ---------------------------------------------- >> David V. Smith, Ph.D. >> Postdoctoral Fellow, Delgado Lab >> Department of Psychology >> Rutgers University >> Newark, NJ 07102 >> ---------------------------------------------- >> > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet > > > >