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.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,DavidOn 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=1Unfortunately, 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,DavidOn 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 LabDepartment of PsychologyRutgers UniversityNewark, 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