QuNex 0.94.4 is now available. Please see release notes below.
* QuNex inline documentation can be now accessed through the `--help`, `-help`, `-h`, `--h`, `-H` and `--H` flags.
* Fixed a bug in the `extract_roi` command that caused crashes in some cases.
* Improved and optimised mapping logic. Resolved an issue where spin-echo or phase-magnitude field map numbers are not assigned correctly when there are incomplete field map pairs.
* Added the ability to enforce bold numbering in the mapping file.
* Added longitudinal FreeSurfer, for this to work you need to use an unreleased version of HCP Pipelines. Contact us if you need this for your work.
* The logic for filtering sessions and subjects is now consistent across the whole suite.
* Added the ability to import Bruker data and mice preprocessing pipelines.
* Logic for filtering sessions is now consistent across the whole suite. You can now use the filter parameter to select a subset of sessions (e.g., the control or the test group, sessions that match a name pattern, etc.).
Hello, I tried to run a singularity container with this new version but it spit out an error when I ran “–env_status”: ERROR: The following environment variable(s) are missing: EDDYCUDADIR, see below.
Also, is it possible to update FSL to version 6.0.5.1? the HCP pipelines for ASL requires this version specifically https://github.com/physimals/hcp-asl. Thank you.
cn2107:~ moana004$ qunex_container --container=qunex/qunex_suite-0.94.4.sif --env_status
cn2107:~ moana004$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.94.4
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
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DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSES' which is a part of the QuNex Suite source code package:
https://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES
---> Setting up Octave
--------------------------------------------------------------
QuNex Environment Status Report
--------------------------------------------------------------
OS Version
----------------------------------------------
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"
QuNex General Environment Variables
----------------------------------------------
QuNexVer : 0.94.4
TOOLS : /opt
QUNEXREPO : qunex
QUNEXPATH : /opt/qunex
QUNEXENV : /opt/env/qunex
TemplateFolder : /opt/qunex/qx_library/data/
QUNEXMCOMMAND : octave -q --no-init-file --eval
Core Dependencies Environment Variables
----------------------------------------------
CONDADIR : /opt/miniconda
FSLDIR : /opt/fsl/fsl
FSLCONFDIR : /panfs/roc/msisoft/fsl/6.0.2/config
FSLGPUDIR : /opt/fsl/fsl/bin
FSL_GPU_SCRIPTS : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu
FSLGPUBinary : /opt/qunex/qx_library/etc/fsl_gpu_binaries
FSL_FIXDIR : /opt/fsl/fix
FREESURFER_HOME : /opt/freesurfer/freesurfer-6.0
FREESURFER_SCHEDULER : /opt/freesurfer/FreeSurferScheduler
WORKBENCHDIR : /opt/workbench/workbench/bin_rh_linux64
CARET7DIR : /opt/workbench/workbench/bin_rh_linux64
AFNIDIR : /opt/AFNI/AFNI
ANTSDIR : /opt/ANTs/ANTs/bin
DCMNIIDIR : /opt/dcm2niix/dcm2niix
DICMNIIDIR : /opt/dicm2nii/dicm2nii
OCTAVEDIR : /opt/octave/octave
OCTAVEPKGDIR : /opt/octave/octavepkg
OCTAVEBINDIR : /opt/octave/octave/bin
RDIR : /opt/R/R
PALMDIR : /opt/palm/palm-o
HCP Pipelines
----------------------------------------------
HCPPIPEDIR : /opt/HCP/HCPpipelines
GRADUNWARPDIR : /opt/gradunwarp/gradunwarp
HCPPIPEDIR_Templates : /opt/HCP/HCPpipelines/global/templates
HCPPIPEDIR_Bin : /opt/HCP/HCPpipelines/global/binaries
HCPPIPEDIR_Config : /opt/HCP/HCPpipelines/global/config
HCPPIPEDIR_PreFS : /opt/HCP/HCPpipelines/PreFreeSurfer/scripts
HCPPIPEDIR_FS : /opt/HCP/HCPpipelines/FreeSurfer/scripts
HCPPIPEDIR_PostFS : /opt/HCP/HCPpipelines/PostFreeSurfer/scripts
HCPPIPEDIR_fMRISurf : /opt/HCP/HCPpipelines/fMRISurface/scripts
HCPPIPEDIR_fMRIVol : /opt/HCP/HCPpipelines/fMRIVolume/scripts
HCPPIPEDIR_tfMRI : /opt/HCP/HCPpipelines/tfMRI/scripts
HCPPIPEDIR_dMRI : /opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts
HCPPIPEDIR_dMRITract : /opt/qunex/bash/qx_utilities/diffusion_tractography/scripts
HCPPIPEDIR_Global : /opt/HCP/HCPpipelines/global/scripts
HCPPIPEDIR_tfMRIAnalysis : /opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts
MSMBINDIR : /opt/MSM_HOCR_v3
HCPPIPEDIR_dMRITractFull : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense
HCPPIPEDIR_dMRILegacy : /opt/qunex/bash/qx_utilities
AutoPtxFolder : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended
EDDYCUDADIR :
ASLDIR : /opt/HCP/HCPpipelines/hcp-asl
Binary / Executable Locations and Versions
----------------------------------------------
HCPpipelines TAG : v4.4.0
HCPpipelines commit : e7a6af936d3a9255a2585d2cc16cdea85454e6ca
FSL Binary : /opt/fsl/fsl/bin/fsl
FSL Version : 6.0.5:9e026117
FreeSurfer Binary : /opt/freesurfer/freesurfer-6.0/bin/freesurfer
FreeSurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
AFNI Binary : /opt/AFNI/AFNI/afni
AFNI Version : Precompiled binary linux_centos_7_64: Jul 26 2022 (Version AFNI_22.2.03 'Marcus Aurelius')
ANTs Binary : /opt/ANTs/ANTs/bin/antsJointFusion
ANTs Version : ANTs Version: 2.3.5.dev1-g6f137
Compiled: Jul 28 2022 02:00:20
dcm2niix Binary : /opt/dcm2niix/dcm2niix/dcm2niix
dcm2niix Version : Chris Rorden's dcm2niiX version v1.0.20190720 (JP2:OpenJPEG) GCC4.8.5 (64-bit Linux)
Octave Binary : /opt/octave/octave/bin/octave
Octave Version : 4.4.1
R Binary : /usr/local/bin/R
R Version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
R required packages : ggplot2
R Package : ggplot2 â3.3.6â
PALM Binary : /opt/palm/palm-o/palm.m
PALM Version : Jun/2021 (github)
wb_command Binary : /opt/workbench/workbench/bin_rh_linux64/wb_command
wb_command Version : Version: 1.5.0
Full Environment Paths
----------------------------------------------
PATH : /usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/ANTs/ANTs/bin:/opt/AFNI/AFNI:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/opt/freesurfer/freesurfer-6.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/panfs/roc/msisoft/freesurfer/6.0.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin
MATLABPATH : /opt/qunex/matlab/qx_mice:/opt/qunex/matlab/qx_utilities/general:/opt/qunex/matlab/qx_mri/stats:/opt/qunex/matlab/qx_mri/img:/opt/qunex/matlab/qx_mri/general:/opt/qunex/matlab/qx_mri/fc:/opt/HCP/HCPpipelines/global/matlab:/opt/HCP/HCPpipelines/global/matlab/cifti-matlab:/opt/HCP/HCPpipelines/global/matlab/icaDim:/opt/HCP/HCPpipelines/global/matlab/nets_spectra:/opt/HCP/HCPpipelines/global/matlab:/opt/fsl/fix:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/dicm2nii/dicm2nii:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/fsl/fsl:/opt/fsl/fsl/bin:
ERROR: The following environment variable(s) are missing: EDDYCUDADIR
I just inspected the code, luckily only the EDDYCUDADIR report is erroneous. Everything gets setup up properly, this is just a false alarm. I already fixed the issue and will try to release a new container this week. That container will also include the updated FSL version, the current one in the container is 6.0.5.