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: on behalf of Joseph Orr
Date: Saturday, June 1, 2019 at 1:00 PM
To: HCP Users
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 Institute for Neuroscience
Texas A University
College Station, TX
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