Hello,
I’m running into problems in trying to set up QuNex for my account on the Grace server at Yale. I’ve been working with Lisa Ji, who is very familiar with QuNex, and neither of us are sure what the problem is. When I try to source the setup script for QuNex, I get the following error/output. We’ve checked that I have permissions to the /gpfs/project/fas/n3/software/ directory and that doesn’t appear to be the problem. I put in a ticket with HPC at Yale about 2 weeks ago and am waiting for a reply. I’ve copied the error below (abbreviated to fit space requirements).
[Qu|Nex software]$ source /gpfs/project/fas/n3/software/gracesetup.sh
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at Yale University Department of Psychiatry
Software Licence Disclaimer:
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Use of this software is subject to the terms and conditions defined by the
Yale University Copyright Policies:
http://ocr.yale.edu/faculty/policies/yale-university-copyright-policy
and the terms and conditions defined in the file ‘LICENSE.txt’ which is
a part of this source code package.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
==> Setting up HPC environment and paths ...
--> You are logged in as mac357 on grace1.grace.hpc.yale.internal
--> Studies folder: /gpfs/project/fas/n3//Studies
--> Software folder: /gpfs/project/fas/n3//software
--> N3 User Home folder: /gpfs/project/fas/n3//Users
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
==> set environment: master
… QUNEXREPO : ${QUNEXREPO}
… QUNEXBRANCH : ${QUNEXBRANCH}
Loading Quantitative Neuroimaging Environment & ToolboX (Qu|Nex) Version: v0.61.17
Logged in as User: mac357
Node info: grace1.grace.hpc.yale.internal
OS: RedHat Linux #1 SMP Tue Jul 21 16:43:24 EDT 2020
Qu|Nex [##graphic deleted by user for space constraints of this posting##]
DEVELOPED & MAINTAINED BY:
Anticevic Lab
MBLab led by Grega Repovs
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined by the
Yale University Copyright Policies:
http://ocr.yale.edu/faculty/policies/yale-university-copyright-policy
and the terms and conditions defined in the file ‘LICENSE.md’ which is
a part of the Qu|Nex Suite source code package:
https://bitbucket.org/hidradev/qunextools/src/master/LICENSE.md
—> Setting up Matlab
/usr/bin/which: no gradient_unwarp.py in [##PATH DELETED FROM ERROR MESSAGE BY USER TO FIT SPACE REQUIREMENTS##]
bash: R: command not found…
–> ERROR in Qu|Nex environment. Run ‘qunex_envstatus’ to check missing variables!
–> Your current environment settings are
… QUNEXREPO=qunex
… QUNEXBRANCH=master
–> Use the following functions to edit your environment
- qxreportenv -> to show the current Qu|Nex clone and environment
- qxshowenvs -> to show the available environments
- qxsetenv -> to set the desired environment
[Grace software]$ qunex_envstatus
Qu|Nex Environment Status Report
OS Version
NAME="Red Hat Enterprise Linux Server"
VERSION="7.7 (Maipo)"
ID="rhel"
ID_LIKE="fedora"
VARIANT="Server"
VARIANT_ID="server"
VERSION_ID="7.7"
PRETTY_NAME="Red Hat Enterprise Linux Server 7.7 (Maipo)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:7.7:GA:server"
HOME_URL="https://www.redhat.com/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.7
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.7"
Qu|Nex General Environment Variables
QuNexVer : 0.61.17
TOOLS : /gpfs/project/fas/n3/software
QUNEXREPO : qunex
QUNEXPATH : /gpfs/project/fas/n3/software/qunex
QUNEXENV : /gpfs/project/fas/n3/software/env/qunex
TemplateFolder : /gpfs/project/fas/n3/software/qunex/library/data/
QUNEXMCOMMAND : matlab -nodisplay -nosplash -r
Core Dependencies Environment Variables
CONDADIR : /gpfs/project/fas/n3/software/miniconda/miniconda-latest
FSLDIR :
FSLGPUDIR : /gpfs/project/fas/n3/software/fsl/fsl-latest/bin
FSLGPUBinary : /gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries
FSL_FIXDIR : /gpfs/project/fas/n3/software/fsl/fix-latest
FREESURFER_HOME : /gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0
FREESURFER_SCHEDULER : /gpfs/project/fas/n3/software/freesurfer/FreeSurferScheduler
WORKBENCHDIR : /gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64
CARET7DIR : /gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64
AFNIDIR : /gpfs/project/fas/n3/software/afni/afni-latest
DCMNIIDIR : /gpfs/project/fas/n3/software/dcm2niix/dcm2niix-latest
DICMNIIDIR : /gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest
MATLABDIR : /gpfs/loomis/apps/avx/software/MATLAB/2017b/bin/matlab
MATLABBINDIR : /gpfs/project/fas/n3/software/matlab/bin
RDIR : /gpfs/loomis/apps/avx/software/R/3.5.3-foss-2018a-X11-20180131/bin/R
PALMDIR : /gpfs/project/fas/n3/software/palm/palm-latest-m
HCP Pipelines Environment Variables
HCPPIPEDIR : /gpfs/project/fas/n3/software/HCP/HCPpipelines
GRADUNWARPDIR : /gpfs/project/fas/n3/software/gradunwarp/gradunwarp-latest
HCPPIPEDIR_Templates : /gpfs/project/fas/n3/software/HCP/HCPpipelines/global/templates
HCPPIPEDIR_Bin : /gpfs/project/fas/n3/software/HCP/HCPpipelines/global/binaries
HCPPIPEDIR_Config : /gpfs/project/fas/n3/software/HCP/HCPpipelines/global/config
HCPPIPEDIR_PreFS : /gpfs/project/fas/n3/software/HCP/HCPpipelines/PreFreeSurfer/scripts
HCPPIPEDIR_FS : /gpfs/project/fas/n3/software/HCP/HCPpipelines/FreeSurfer/scripts
HCPPIPEDIR_PostFS : /gpfs/project/fas/n3/software/HCP/HCPpipelines/PostFreeSurfer/scripts
HCPPIPEDIR_fMRISurf : /gpfs/project/fas/n3/software/HCP/HCPpipelines/fMRISurface/scripts
HCPPIPEDIR_fMRIVol : /gpfs/project/fas/n3/software/HCP/HCPpipelines/fMRIVolume/scripts
HCPPIPEDIR_tfMRI : /gpfs/project/fas/n3/software/HCP/HCPpipelines/tfMRI/scripts
HCPPIPEDIR_dMRI : /gpfs/project/fas/n3/software/HCP/HCPpipelines/DiffusionPreprocessing/scripts
HCPPIPEDIR_dMRITract : /gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractography/scripts
HCPPIPEDIR_Global : /gpfs/project/fas/n3/software/HCP/HCPpipelines/global/scripts
HCPPIPEDIR_tfMRIAnalysis : /gpfs/project/fas/n3/software/HCP/HCPpipelines/TaskfMRIAnalysis/scripts
MSMBINDIR : /gpfs/project/fas/n3/software/MSM_HOCR_v3/Centos
HCPPIPEDIR_dMRITracFull : /gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense
HCPPIPEDIR_dMRILegacy : /gpfs/project/fas/n3/software/qunex/connector/functions
AutoPtxFolder : /gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/autoPtx_HCP_extended
EDDYCUDADIR : /gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/eddy_cuda
Binary / Executable Locations and Versions
HCPpipelines : Post-v4.3.0
HCPpipelines TAG : v4.3.0-rc.1
HCPpipelines commit : cd8f164d51cb116120b5236ac1efdb9fda66d7ed
FSL Binary :
FSL Version : Binary not found!
FreeSurfer Binary :
FreeSurfer Version : Binary not found!
AFNI Binary :
AFNI Version : Binary not found!
dcm2niix Binary :
dcm2niix Version : Binary not found!
dicm2nii Binary : /gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest/dicm2nii.m
dicm2nii Version : # DICOM to NIfTI conversion, DICOM and NIfTI tools, NIfTI visualization (version 2018.12.31)
FIX Binary :
FIX Version : Binary not found!
/usr/bin/which: no gradient_unwarp.py in (/gpfs/project/fas/n3/software/qunex/library/bin/:/gpfs/loomis/apps/avx/software/R/3.5.3-foss-2018a-X11-20180131/bin:/gpfs/loomis/apps/avx/software/MATLAB/2017b:/gpfs/loomis/apps/avx/software/MATLAB/2017b/…/MDCE/MDCE_SCRIPTS/bin:/gpfs/loomis/apps/avx/software/MATLAB/2017b/bin:/gpfs/loomis/apps/avx/software/miniconda/4.7.12:/gpfs/loomis/apps/avx/software/miniconda/4.7.12/bin:/gpfs/loomis/apps/avx/software/Octave/4.2.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/GraphicsMagick/1.3.28-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12/bin:/gpfs/loomis/apps/avx/software/LibTIFF/4.0.9-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/SuiteSparse/5.1.2-foss-2018a-METIS-5.1.0/bin:/gpfs/loomis/apps/avx/software/METIS/5.1.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/HDF5/1.10.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Qhull/2015.2-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Java/1.8.0_92:/gpfs/loomis/apps/avx/software/Java/1.8.0_92/bin:/gpfs/loomis/apps/avx/software/gnuplot/5.2.2-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Qt5/5.10.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/gperf/3.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/DBus/1.13.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NSS/3.39-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NSPR/4.20-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Pango/1.41.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/HarfBuzz/1.7.5-foss-2018a/bin:/gpfs/loomis/apps/avx/software/libgd/2.2.5-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/cairo/1.14.12-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/GLib/2.54.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/util-linux/2.31.1-GCCcore-6.4.0/sbin:/gpfs/loomis/apps/avx/software/util-linux/2.31.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/gettext/0.19.8.1-GCCcore-6.4.0-libxml2-2.9.7/bin:/gpfs/loomis/apps/avx/software/GLPK/4.65-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/FLTK/1.3.4-foss-2018a/bin:/gpfs/loomis/apps/avx/software/xprop/1.2.2-GCCcore-6.4.0-X11-20180131/bin:/gpfs/loomis/apps/avx/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NASM/2.13.03-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/LLVM/5.0.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/nettle/3.4-foss-2018a/bin:/gpfs/loomis/apps/avx/software/cURL/7.58.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/PCRE/8.41-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/X11/20180131-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/fontconfig/2.12.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/freetype/2.9-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libpng/1.6.34-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/expat/2.2.5-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Python/2.7.14-foss-2018a/bin:/gpfs/loomis/apps/avx/software/SQLite/3.21.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Tcl/8.6.8-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libreadline/7.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/ncurses/6.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/bzip2/1.0.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/FFTW/3.3.7-gompi-2018a/bin:/gpfs/loomis/apps/avx/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/bin:/gpfs/loomis/apps/avx/software/OpenMPI/2.1.2-GCC-6.4.0-2.28-hdr/bin:/gpfs/loomis/apps/avx/software/hwloc/1.11.8-GCCcore-6.4.0/sbin:/gpfs/loomis/apps/avx/software/hwloc/1.11.8-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libxml2/2.9.7-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/XZ/5.2.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/numactl/2.0.11-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/binutils/2.28-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/GCCcore/6.4.0/bin:/gpfs/loomis/bin:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/probtrackx_gpu_cuda_7.0:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu/bin:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu/lib:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu:/usr/local/cuda-7.5/bin:/gpfs/project/fas/n3/software/bin:/gpfs/project/fas/n3/software/olib:/usr/local/bin:/gpfs/project/fas/n3/software/qunex/nitools:/gpfs/project/fas/n3/software/qunex/library/bin:/gpfs/project/fas/n3/software/qunex/niutilities:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/eddy_cuda:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/autoPtx_HCP_extended:/gpfs/project/fas/n3/software/qunex/connector/functions:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractography/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/tfMRI/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/fMRIVolume/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/fMRISurface/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/PostFreeSurfer/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/FreeSurfer/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/PreFreeSurfer/scripts:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/config:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/binaries:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/templates:/gpfs/project/fas/n3/software/gradunwarp/gradunwarp-latest/gradunwarp/core:/gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64:/gpfs/project/fas/n3/software/HCP/HCPpipelines:/gpfs/project/fas/n3/software/HCP/HCPpipelines/MSMConfig:/gpfs/project/fas/n3/software/qunex/niutilities/templates:/gpfs/project/fas/n3/software/qunex/library/data:/gpfs/project/fas/n3/software/qunex/library/data/atlases/HCP:/gpfs/project/fas/n3/software/R/R-latest:/gpfs/project/fas/n3/software/matlab/bin:/gpfs/project/fas/n3/software/octave/octave-latest/bin:/gpfs/project/fas/n3/software/dcm2niix/dcm2niix-latest:/gpfs/project/fas/n3/software/dcm2niix/dcm2niix-latest/build/bin:/gpfs/project/fas/n3/software/afni/afni-latest:/gpfs/project/fas/n3/software/palm/palm-latest-m:/gpfs/project/fas/n3/software/freesurfer/FreeSurferScheduler:/gpfs/project/fas/n3/software/fsl/fsl-latest/bin:/gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0/bin:/gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0/fsfast/bin:/gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0/tktools:/gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0/mni/bin:/gpfs/project/fas/n3/software/freesurfer/freesurfer-6.0:/gpfs/project/fas/n3/software/lib/bin:/gpfs/project/fas/n3/software/lib/lib:/gpfs/project/fas/n3/software/miniconda/miniconda-latest/bin:/opt/TurboVNC/bin:/usr/lib64/qt-3.3/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/bin)
Gradunwarp Binary :
/usr/bin/which: no gradient_unwarp.py in (/gpfs/project/fas/n3/software/qunex/library/bin/:/gpfs/loomis/apps/avx/software/R/3.5.3-foss-2018a-X11-20180131/bin:/gpfs/loomis/apps/avx/software/MATLAB/2017b:/gpfs/loomis/apps/avx/software/MATLAB/2017b/…/MDCE/MDCE_SCRIPTS/bin:/gpfs/loomis/apps/avx/software/MATLAB/2017b/bin:/gpfs/loomis/apps/avx/software/miniconda/4.7.12:/gpfs/loomis/apps/avx/software/miniconda/4.7.12/bin:/gpfs/loomis/apps/avx/software/Octave/4.2.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/GraphicsMagick/1.3.28-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12/bin:/gpfs/loomis/apps/avx/software/LibTIFF/4.0.9-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/SuiteSparse/5.1.2-foss-2018a-METIS-5.1.0/bin:/gpfs/loomis/apps/avx/software/METIS/5.1.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/HDF5/1.10.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Qhull/2015.2-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Java/1.8.0_92:/gpfs/loomis/apps/avx/software/Java/1.8.0_92/bin:/gpfs/loomis/apps/avx/software/gnuplot/5.2.2-foss-2018a/bin:/gpfs/loomis/apps/avx/software/Qt5/5.10.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/gperf/3.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/DBus/1.13.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NSS/3.39-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NSPR/4.20-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Pango/1.41.1-foss-2018a/bin:/gpfs/loomis/apps/avx/software/HarfBuzz/1.7.5-foss-2018a/bin:/gpfs/loomis/apps/avx/software/libgd/2.2.5-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/cairo/1.14.12-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/GLib/2.54.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/util-linux/2.31.1-GCCcore-6.4.0/sbin:/gpfs/loomis/apps/avx/software/util-linux/2.31.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/gettext/0.19.8.1-GCCcore-6.4.0-libxml2-2.9.7/bin:/gpfs/loomis/apps/avx/software/GLPK/4.65-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/FLTK/1.3.4-foss-2018a/bin:/gpfs/loomis/apps/avx/software/xprop/1.2.2-GCCcore-6.4.0-X11-20180131/bin:/gpfs/loomis/apps/avx/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/NASM/2.13.03-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/LLVM/5.0.1-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/nettle/3.4-foss-2018a/bin:/gpfs/loomis/apps/avx/software/cURL/7.58.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/PCRE/8.41-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/X11/20180131-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/fontconfig/2.12.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/freetype/2.9-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libpng/1.6.34-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/expat/2.2.5-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Python/2.7.14-foss-2018a/bin:/gpfs/loomis/apps/avx/software/SQLite/3.21.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/Tcl/8.6.8-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libreadline/7.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/ncurses/6.0-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/bzip2/1.0.6-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/FFTW/3.3.7-gompi-2018a/bin:/gpfs/loomis/apps/avx/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/bin:/gpfs/loomis/apps/avx/software/OpenMPI/2.1.2-GCC-6.4.0-2.28-hdr/bin:/gpfs/loomis/apps/avx/software/hwloc/1.11.8-GCCcore-6.4.0/sbin:/gpfs/loomis/apps/avx/software/hwloc/1.11.8-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/libxml2/2.9.7-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/XZ/5.2.3-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/numactl/2.0.11-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/binutils/2.28-GCCcore-6.4.0/bin:/gpfs/loomis/apps/avx/software/GCCcore/6.4.0/bin:/gpfs/loomis/bin:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/probtrackx_gpu_cuda_7.0:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu/bin:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu/lib:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/bedpostx_gpu_cuda_7.5/bedpostx_gpu:/usr/local/cuda-7.5/bin:/gpfs/project/fas/n3/software/bin:/gpfs/project/fas/n3/software/olib:/usr/local/bin:/gpfs/project/fas/n3/software/qunex/nitools:/gpfs/project/fas/n3/software/qunex/library/bin:/gpfs/project/fas/n3/software/qunex/niutilities:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries/eddy_cuda:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/fsl_gpu_binaries:/gpfs/project/fas/n3/software/qunex/connector/functions/DiffusionTractographyDense/autoPtx_HCP_extended:/gpf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Gradunwarp Version : Binary not found!
MSM Binary : /gpfs/project/fas/n3/software/MSM_HOCR_v3/Centos/msm
MSM Version : Part of FSL (ID: 6.0.2:3b4d64ae)
Matlab Binary : /gpfs/loomis/apps/avx/software/MATLAB/2017b/bin/matlab
Matlab Version : /gpfs/loomis/apps/avx/software/MATLAB/2017b/bin/matlab
R Binary : /gpfs/loomis/apps/avx/software/R/3.5.3-foss-2018a-X11-20180131/bin/R
R Version : R version 3.5.3 (2019-03-11) -- "Great Truth"
R required packages : ggplot2
R Package : ggplot2 ‘3.2.1’
PALM Binary : /gpfs/project/fas/n3/software/palm/palm-latest-m/palm.m
PALM Version : Oct/2018 (version alpha112)
wb_command Binary :
wb_command Version : Binary not found!
Full Environment Paths
PATH : [##deleted by user for space constaints##]
PYTHONPATH :
MATLABPATH : /gpfs/project/fas/n3/software/qunex/nitools/stats:/gpfs/project/fas/n3/software/qunex/nitools/img:/gpfs/project/fas/n3/software/qunex/nitools/general:/gpfs/project/fas/n3/software/qunex/nitools/fcMRI:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab/:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/library/data/:/gpfs/project/fas/n3/software/qunex/library/data/atlases/HCP:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest:/gpfs/project/fas/n3/software/palm/palm-latest-m:/gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64:/gpfs/project/fas/n3/software/fsl/fsl-latest:/gpfs/project/fas/n3/software/fsl/fsl-latest/bin:/gpfs/project/fas/n3/software/qunex/nitools/stats:/gpfs/project/fas/n3/software/qunex/nitools/img:/gpfs/project/fas/n3/software/qunex/nitools/general:/gpfs/project/fas/n3/software/qunex/nitools/fcMRI:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab/:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/library/data/:/gpfs/project/fas/n3/software/qunex/library/data/atlases/HCP:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest:/gpfs/project/fas/n3/software/palm/palm-latest-m:/gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64:/gpfs/project/fas/n3/software/fsl/fsl-latest:/gpfs/project/fas/n3/software/fsl/fsl-latest/bin:/gpfs/project/fas/n3/software/qunex/nitools/stats:/gpfs/project/fas/n3/software/qunex/nitools/img:/gpfs/project/fas/n3/software/qunex/nitools/general:/gpfs/project/fas/n3/software/qunex/nitools/fcMRI:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab/:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/library/data/:/gpfs/project/fas/n3/software/qunex/library/data/atlases/HCP:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest:/gpfs/project/fas/n3/software/palm/palm-latest-m:/gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64:/gpfs/project/fas/n3/software/fsl/fsl-latest:/gpfs/project/fas/n3/software/fsl/fsl-latest/bin:/gpfs/project/fas/n3/software/qunex/nitools/stats:/gpfs/project/fas/n3/software/qunex/nitools/img:/gpfs/project/fas/n3/software/qunex/nitools/general:/gpfs/project/fas/n3/software/qunex/nitools/fcMRI:/gpfs/project/fas/n3/software/HCP/HCPpipelines/global/matlab/:/gpfs/project/fas/n3/software/fsl/fix-latest:/gpfs/project/fas/n3/software/qunex/library/data/:/gpfs/project/fas/n3/software/qunex/library/data/atlases/HCP:/gpfs/project/fas/n3/software/qunex/connector:/gpfs/project/fas/n3/software/dicm2nii/dicm2nii-latest:/gpfs/project/fas/n3/software/palm/palm-latest-m:/gpfs/project/fas/n3/software/workbench/workbench-latest/bin_rh_linux64:/gpfs/project/fas/n3/software/fsl/fsl-latest:/gpfs/project/fas/n3/software/fsl/fsl-latest/bin:
ERROR: The following environment variable(s) are missing: FSLDIR