Hi Tim,
Thank you for the help with the workbench and the code. Yes, it is a mac osx. Sorry for the mix up. Also, I can get the first two commands to work for "MEAN" and "STDEV", but the last command gives me an error message: wb_command -volume-math '((x - mean) / stdev)' normalized.nii.gz -fixnan 0 -var x <input> -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat ERROR: volume file for variable 'mean' has 1 subvolume(s), but previous volume files have 1200 subvolume(s) requested to be used Any help would be appreciated. best, Jason Jason S. Nomi, Ph.D. Post-Doctoral Researcher (BCCL Lab) Department of Psychology University of Miami 5151 San Amaro Drive: Room 114A Website: http://www.psy.miami.edu/bccl/ Email: jxn...@miami.edu ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Monday, October 27, 2014 5:38 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Using Connectome Workbench Commands Inline replies. Tim On Mon, Oct 27, 2014 at 10:26 AM, Nomi, Jason <jxn...@miami.edu<mailto:jxn...@miami.edu>> wrote: Dear Experts, I am trying to use the workbench commands but cannot get them to work. After opening the “wb_command” file in my linux terminal, I get the message printed below. Linux terminal? The output shows that you successfully executed the Mac OS X binary, is there a linux system involved? However, none of the commands work and nothing comes up when I type in the command by itself to get help. I have tried all the various combinations. With the “-“, without it. With “wb_command” to start, without it, etc. Try entering this at the command line: /Applications/workbench/bin_macosx64/wb_command -volume-reduce If you want to use it without entering that path each time, you'll need to add "/Applications/workbench/bin_macosx64/" to your PATH environment variable. How to do this depends on what shell you are using. Also, I would like to conduct variance normalization on some of the .nii files from the ICA-Fix dataset. Would using the command, “-volume-reduce" with the VARIANCE operation accomplish this? No, among other things, variance is nonlinear with the spread of the data. If the files you are looking at end in .dtseries.nii, they are not volume files, but rather CIFTI files (there are other 2-part extensions that signify CIFTI files, but ICA-FIX should be using dtseries). This thread contains the steps for normalizing (including demeaning) along timeseries while in CIFTI format: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html Similar commands apply if you are actually dealing with volume file timeseries: wb_command -volume-reduce <input> MEAN mean.nii.gz wb_command -volume-reduce <input> STDEV stdev.nii.gz wb_command -volume-math '(x - mean) / stdev' normalized.nii.gz -fixnan 0 -var x <input> -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat Thank you very much for you help. best, Jason UM-46JNG5RP:~ admin$ /Applications/workbench/bin_macosx64/wb_command ; exit & Why do you have "; exit &" on the end? Connectome Workbench Version: 1.0 Qt Compiled Version: 4.8.3 Qt Runtime Version: 4.8.3 commit: dfd2086d37612ccf2369b85b5f5f0f5987369339 commit date: 2014-09-09 13:23:57 -0500 Compiler: clang2++ (/usr/local/clang-openmp-opt/llvm/build/Release/bin) Compiler Version: Compiled Debug: NO Operating System: Apple OSX Information options: -help print this help info -arguments-help explain how to read the help info for subcommands -version print version information only -list-commands print all non-information (processing) subcommands -all-commands-help print all non-information (processing) subcommands and their help info - VERY LONG Global options (can be added to any command): -disable-provenance don't generate provenance info in output files If the first argument is not recognized, all processing commands that start with the argument are displayed _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
