Thanks. I did and they helped. The problem seams to be the required version for packages: 'kernlab' version 0.9.24 'ROCR' version 1.0.7 'class' version 7.3.14 'party' version 1.0.25 'e1071' version 1.6.7 'randomForest' version 4.6.12
> On Nov 6, 2017, at 9:34 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > I would ask specifically on the FSL list again as they are the primary > support for FIX. > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Monday, November 6, 2017 at 8:31 PM > To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Cc: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] HCP_hp2000.RData > > Thanks, Matt. > > I am still getting the same problem. What version of R and package party are > you using or is recommended? > I checked also in the FSL list and this problem has been posted but not > solution was provided. > > Thank you, > -L > >> On Nov 6, 2017, at 11:54 AM, Glasser, Matthew <glass...@wustl.edu >> <mailto:glass...@wustl.edu>> wrote: >> >> I’m not an expert in R, so I’m not sure. I think that it does some >> compiling and other things on my machine, but perhaps if you don’t compile >> that is all that is needed. You could test ICA+FIX again and see if the >> error is resolved. >> >> Peace, >> >> Matt. >> >> From: Marta Moreno <mmorenoort...@icloud.com >> <mailto:mmorenoort...@icloud.com>> >> Date: Monday, November 6, 2017 at 10:51 AM >> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> >> Cc: HCP Users <hcp-users@humanconnectome.org >> <mailto:hcp-users@humanconnectome.org>> >> Subject: Re: [HCP-Users] HCP_hp2000.RData >> >> Thanks again, Matt. >> >> I went through required packages again as suggested, a common output in R is >> the following (for all packages): as root, >> "> install.packages("randomForest", dependencies=TRUE) >> trying URL >> 'https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/randomForest_4.6-12.tgz >> >> <https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/randomForest_4.6-12.tgz>' >> Content type 'application/x-gzip' length 176377 bytes (172 KB) >> ================================================== >> downloaded 172 KB >> The downloaded binary packages are in >> /tmp/RtmpP65gVF/downloaded_packages” >> >> Should I go over each package to install it or this message includes >> installation? >> >> Thank you, >> >> -L >> >> >>> On Nov 6, 2017, at 10:31 AM, Glasser, Matthew <glass...@wustl.edu >>> <mailto:glass...@wustl.edu>> wrote: >>> >>> You could ask on the FSL list, but I think it would make sense to go >>> through the setup instructions again and make sure you aren’t missing any >>> of the required R packages. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Marta Moreno <mmorenoort...@icloud.com >>> <mailto:mmorenoort...@icloud.com>> >>> Date: Monday, November 6, 2017 at 9:29 AM >>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> >>> Cc: HCP Users <hcp-users@humanconnectome.org >>> <mailto:hcp-users@humanconnectome.org>> >>> Subject: Re: [HCP-Users] HCP_hp2000.RData >>> >>> Thank you, Matt. I found the only one and following error in >>> Results/RS_fMRI_2/RS_fMRI_2_hp2000.ica: >>> >>> "Error in ctreefit(object = object, controls = controls, weights = weights, >>> : >>> no slot of name "remove_weights" for this object of class >>> "TreeGrowControl" >>> Calls: eval -> eval -> <Anonymous> -> ctreefit -> .Call >>> Execution halted” >>> >>> Any idea what should I do to fix this problem? I do not have R-devel >>> installed, is this required and/or related to this problem? >>> >>> Thank you, >>> >>> -L >>> >>> >>> >>> >>> >>>> On Nov 4, 2017, at 4:55 PM, Glasser, Matthew <glass...@wustl.edu >>>> <mailto:glass...@wustl.edu>> wrote: >>>> >>>> You will need to look into the logs more carefully (i.e. in subfolders of >>>> the FIX folder) and you will likely find some issue with the R packages >>>> you have installed. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org >>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno >>>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> >>>> Date: Saturday, November 4, 2017 at 3:28 PM >>>> To: HCP Users <hcp-users@humanconnectome.org >>>> <mailto:hcp-users@humanconnectome.org>> >>>> Subject: [HCP-Users] HCP_hp2000.RData >>>> >>>> Dear experts, >>>> >>>> I am getting the following error running hip_fix, my RSfMRI data is >>>> similar to HCP data but I am getting the following error running hcp_fix >>>> RS_fMRI_2/RS_fMRI_2.nii.gz 2000: >>>> >>>> "FIX Classifying components in Melodic directory: RS_fMRI_2_hp2000.ica >>>> using training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData >>>> and threshold 10 >>>> No valid labelling file specified" >>>> >>>> I checked the settings and everything looks good. I do not see errors in >>>> <subject.ica>/.fix.log. Any idea what might be the problem? >>>> >>>> Thank you, >>>> >>>> -L >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
