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Looks like you are both missing R packages? Peace, Matt. From: Michel Thiebaut <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Wednesday, July 2, 2014 at 11:14 AM To: <[log in to unmask]> Subject: Re: [FSL] FIX issue Don't know if it helps but my .fix_2b_predict.log says: R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.1.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > library(party) Loading required package: grid Loading required package: zoo Error: package zooš could not be loaded In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called zooš Execution halted On Wed, Jul 2, 2014 at 5:03 PM, Ricarda Menke <[log in to unmask]> wrote: > Hi Ludo, > > I'm experiencing a similar problem. I also didn't get a .fix file, but there > is a .fix_2b_predict.log file that contains the following message (even though > the coin.so seems to exist in the specified directory): > ----- > cat .fix_2b_predict.log > > R version 3.1.0 (2014-04-10) -- "Spring Dance" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-redhat-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> > >> > library(party) > Loading required package: survival > Loading required package: splines > Loading required package: grid > Loading required package: modeltools > Loading required package: stats4 > Loading required package: coin > Loading required package: mvtnorm > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object '/opt/fmrib/R/site-library/coin/libs/coin.so': > libRblas.so: cannot open shared object file: No such file or directory > Error: package coinš could not be loaded > Execution halted > ----- > > Cheers, > Ricarda > > > > On 2 Jul 2014, at 16:49, Michel Thiebaut <[log in to unmask]> wrote: > >> Dear Ludovica their is no .fix file in the folder unfortunately >> (I tried open -a TextEdit .fix) >> >> I also installed R with all the toolboxes required. I have no idea what to >> try next. >> Thanks a lot for your help, >> >> michel >> >> >> On Wed, Jul 2, 2014 at 4:27 PM, Ludovica Griffanti >> <[log in to unmask]> wrote: >>> Hi Michel, >>> try to have a look at the file: output.ica/.fix >>> It should be a log file containing general errors in the whole fix pipeline. >>> I guess this time is a problem related to the classification part (done with >>> R) >>> Hope that helps. >>> >>> Best, >>> Ludovica >>> >>> --- >>> Dr Ludovica Griffanti, PhD >>> Analysis Postdoctoral Research Assistant >>> Oxford Centre for Functional MRI of the Brain (FMRIB) >>> Nuffield Department of Clinical Neurosciences, University of Oxford >>> John Radcliffe Hospital >>> Oxford, OX3 9DU, UK >>> email: [log in to unmask] >>> >>> On 2 Jul 2014, at 12:41, Michel Thiebaut <[log in to unmask]> wrote: >>> >>>> Thanks a lot Ludovica, >>>> I did correct Matlab setup and now the output.ica/fix/logMatlab.txt does >>>> not report any error. >>>> >>>> but still fix doesn't work and report >>>> >>>> Michels-MacBook-Air:testfix michelthiebautdeschotten$ >>>> /usr/local/fix1.06/fix output.ica >>>> /usr/local/fix1.06/training_files/Standard.RData 20 -m >>>> FIX Feature extraction for Melodic output directory: output.ica >>>> create edge masks >>>> run FAST >>>> registration of standard space masks >>>> extract features >>>> FIX Classifying components in Melodic directory: output.ica using training >>>> file: /usr/local/fix1.06/training_files/Standard.RData and threshold 20 >>>> No valid labelling file specified >>>> >>>> Any other suggestion? >>>> thanks a lot for your time, >>>> >>>> kind regards, >>>> >>>> michel >>>> >>>> >>>> On Wed, Jul 2, 2014 at 9:44 AM, Ludovica Griffanti >>>> <[log in to unmask]> wrote: >>>>> Hi Michel, >>>>> the problem is during features extraction, which is done with >>>>> MATLAB/Octave. >>>>> You can find more details about the error in the file: >>>>> output.ica/fix/logMatlab.txt >>>>> You will probably have to check your Matlab/Octave setup following the >>>>> instruction in the README file provided with the tool. >>>>> >>>>> see also: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406&L=FSL&F=&S=&X=FA353 >>>>> 758F0C69828D5&Y=ludovica.griffanti%40ndcn.ox.ac.uk&P=431512 >>>>> >>>>> Best, >>>>> Ludovica >>>>> >>>>> --- >>>>> Dr Ludovica Griffanti, PhD >>>>> Analysis Postdoctoral Research Assistant >>>>> Oxford Centre for Functional MRI of the Brain (FMRIB) >>>>> Nuffield Department of Clinical Neurosciences, University of Oxford >>>>> John Radcliffe Hospital >>>>> Oxford, OX3 9DU, UK >>>>> email: [log in to unmask] >>>>> >>>>> On 1 Jul 2014, at 19:37, Michel Thiebaut <[log in to unmask]> >>>>> wrote: >>>>> >>>>>> Dear Experts, >>>>>> >>>>>> I tried to launch FIX today following the instructions online but it did >>>>>> not produce the final filtered functional data. >>>>>> >>>>>> This is the message the terminal gives >>>>>> >>>>>> /usr/local/fix1.06/fix output.ica >>>>>> /usr/local/fix1.06/training_files/Standard.RData 20 -m >>>>>> >>>>>> FIX Feature extraction for Melodic output directory: output.ica >>>>>> create edge masks >>>>>> run FAST >>>>>> registration of standard space masks >>>>>> extract features >>>>>> FIX Classifying components in Melodic directory: output.ica using >>>>>> training file: /usr/local/fix1.06/training_files/Standard.RData and >>>>>> threshold 20 >>>>>> FIX features not already generated, so creating them now. >>>>>> FIX Feature extraction for Melodic output directory: output.ica >>>>>> create edge masks >>>>>> run FAST >>>>>> registration of standard space masks >>>>>> extract features >>>>>> No valid labelling file specified >>>>>> >>>>>> I was wondering whether you could tell me what I did wrong. >>>>>> Thanks a lot for your time. >>>>>> Kind regards >>>>>> >>>>>> michel >>>>> >>>> >>> >> >