That is the error I would expect if you removed the -repeat after the -var option for mean (yes, it needs 2 -repeat options, they each associate with one -var option) - could you paste the command you actually ran?
Tim On Tue, Oct 28, 2014 at 11:30 AM, Nomi, Jason <[email protected]> wrote: > 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: [email protected] > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *Sent:* Monday, October 27, 2014 5:38 PM > *To:* Nomi, Jason > *Cc:* [email protected] > *Subject:* Re: [HCP-Users] Using Connectome Workbench Commands > > Inline replies. > > Tim > > On Mon, Oct 27, 2014 at 10:26 AM, Nomi, Jason <[email protected]> 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/[email protected]/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 >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
