I’m running into an issue on the 1.0.1 container for general_extract_glm_volumes. When it tries to read the file listed in the list it gives this error:
---> processing session: NDARINV08R2PTT1_baselineYear1Arm1
Matlab Error! Processing Failed!
regexp: the input string is invalid UTF-8
It works correctly with the same files/params when I force it to use Matlab or use a container prior to 0.99.3 :
---> processing session: NDARINV08R2PTT1_baselineYear1Arm1
---> Embedding meta list [code 64]
---> saving data in a single file, sorted by session
---> DONE
As such I assume it’s related to Octave.
Don’t know exactly what the issue is but seems to occur when it tries to create an nimage object on line 166 in matlab/qx_mri/general/general_extract_glm_volumes.m :
glm = nimage(list.session(1).glm);
PS: Unrelated but there seems to be repeated code in that file (lines 119-130 vs. 136-147) which can be probably be removed
Call:
qunex_container general_extract_glm_volumes \
--flist="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/mid_1.list" \
--effects="LR,Neutral" \
--saveoption="by_session" \
--values="raw" \
--verbose='true' \
--outf="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-1.0.1.sif"
To force it to use matlab on Grace I add:
--bash_post="QUNEXMCOMMAND='/vast/palmer/apps/avx2/software/MATLAB/2023a/bin/matlab -nodisplay -nosplash -r';export QUNEXMCOMMAND"
Input List:
session id: NDARINV08R2PTT1_baselineYear1Arm1
glm: /gpfs/gibbs/pi/n3/Studies/ABCD/site21/sessions/NDARINV08R2PTT1_baselineYear1Arm1/images/functional/bold_Atlas_conc_mid_s_res-me_MID_test_Bcoeff.dtseries.nii
Error Log:
---> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXEXTENSIONS QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR PYLIBDIR FSLDIR FSLBINDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_FS_CUSTOM HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder EDDYCUDA 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 ANTSDIR CUDIMOT
========================================================================
Generated by QuNex
------------------------------------------------------------------------
Version: 1.0.1 [QIO]
User: sab322
System: r816u15n12.grace.ycrc.yale.edu
OS: Debian Linux #1 SMP Mon Sep 30 16:14:54 EDT 2024
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Mind & Brain Lab, University of Ljubljana
Cho Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
QuNex LICENSES which can be found in the LICENSES folder of the QuNex
repository or at https://qunex.yale.edu/qunex-registration
========================================================================
---> Setting up Octave
.......................... Running QuNex v1.0.1 [QIO] ..........................
--- Full QuNex call for command: general_extract_glm_volumes
qunex general_extract_glm_volumes flist="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/mid_1.list" effects="LR,Neutral" saveoption="by_session" values="raw" verbose="true" outf="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/"
---------------------------------------------------------
Running:
>>> general_extract_glm_volumes('/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/mid_1.list', '/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/', 'LR,Neutral', [], 'by_session', 'raw', true, '')
---> checking file list
---> checking file list
---> processing session: NDARINV08R2PTT1_baselineYear1Arm1
Matlab Error! Processing Failed!
regexp: the input string is invalid UTF-8
ERROR: general_extract_glm_volumes failed! Please check output / log!
Pass Log:
---> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXEXTENSIONS QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR PYLIBDIR FSLDIR FSLBINDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_FS_CUSTOM HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder EDDYCUDA 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 ANTSDIR CUDIMOT
========================================================================
Generated by QuNex
------------------------------------------------------------------------
Version: 1.0.1 [QIO]
User: sab322
System: r816u15n12.grace.ycrc.yale.edu
OS: Debian Linux #1 SMP Mon Sep 30 16:14:54 EDT 2024
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Mind & Brain Lab, University of Ljubljana
Cho Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
QuNex LICENSES which can be found in the LICENSES folder of the QuNex
repository or at https://qunex.yale.edu/qunex-registration
========================================================================
---> Setting up Octave
.......................... Running QuNex v1.0.1 [QIO] ..........................
--- Full QuNex call for command: general_extract_glm_volumes
qunex general_extract_glm_volumes flist="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/mid_1.list" effects="LR,Neutral" saveoption="by_session" values="raw" verbose="true" outf="/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/"
---------------------------------------------------------
Running:
>>> general_extract_glm_volumes('/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/mid_1.list', '/gpfs/gibbs/pi/n3/Studies/ABCD/site21/analysis_fmri_task/mid/test_LR_Neutral_t/test/', 'LR,Neutral', [], 'by_session', 'raw', true, '')
< M A T L A B (R) >
Copyright 1984-2023 The MathWorks, Inc.
R2023a Update 2 (9.14.0.2254940) 64-bit (glnxa64)
April 17, 2023
Warning: X does not support locale C.UTF-8
To get started, type doc.
For product information, visit www.mathworks.com.
---> checking file list
---> checking file list
---> processing session: NDARINV08R2PTT1_baselineYear1Arm1
---> Embedding meta list [code 64]
---> saving data in a single file, sorted by session
---> DONE
---> Successful completion of task