Thanks for posting the solution here as well. Matt.
From: Marta Moreno <[email protected]<mailto:[email protected]>> Date: Tuesday, November 7, 2017 at 12:20 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: HCP Users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP_hp2000.RData 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 <[email protected]<mailto:[email protected]>> wrote: I would ask specifically on the FSL list again as they are the primary support for FIX. Matt. From: Marta Moreno <[email protected]<mailto:[email protected]>> Date: Monday, November 6, 2017 at 8:31 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: HCP Users <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Date: Monday, November 6, 2017 at 10:51 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: HCP Users <[email protected]<mailto:[email protected]>> 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' 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Date: Monday, November 6, 2017 at 9:29 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: HCP Users <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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: <[email protected]<mailto:[email protected]>> on behalf of Marta Moreno <[email protected]<mailto:[email protected]>> Date: Saturday, November 4, 2017 at 3:28 PM To: HCP Users <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
