It sounds like there might be both Workbench and PALM bugs here. Perhaps you could upload the data somewhere (off list if needed), so Tim and Anderson could take a look?
Matt. From: <[email protected]> on behalf of Joseph Orr <[email protected]> Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users <[email protected]> Subject: [HCP-Users] pdconn analysis problems I have a pdconn input (cortical ptseries by subcortical dtseries) that I'd like to analyze with PALM, but I'm having some trouble. I only found one old post related to this, but the only suggestion was to use -transpose data flag in palm. When palm tries to read in the pdconn, I get an error "Undefined function or variable 'Y'". The command line output is below. I tried with the data transposed and not, but I get the same error. I tried to separate the pdconn to just the volume, but this yielded a segmentation error: ($ wb_command -cifti-separate input.pdconn.nii ROW -volume-all test /Applications/workbench/bin_macosx64/wb_command: line 14: 1248 Segmentation fault: 11 "$directory"/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command "$@"). Are there any additional commands I can run on a pdconn to separate each parcel and have a series of dconn files? I'd be interested in doing this in order to compare the dense connectivity maps for different parcels. Thanks! Joe Command line output for palm Running PALM alpha115 using MATLAB 9.5.0.1067069 (R2018b) Update 4 with the following options: -i input.pdconn.nii -transposedata -o palm -d design.mat -t design.con -T Found FSL in /usr/local/fsl Found FreeSurfer in /Applications/freesurfer Found HCP Workbench executable in /Applications/workbench/bin_macosx64/wb_command Reading input 1/1: input.pdconn.nii Error using palm_ready (/Users/josephorr/Documents/MATLAB/palm-alpha115/palm_ready.m:141) Undefined function or variable 'Y' -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
