[RESOLVED] Error running matlab general_compute_bold_stats

Description:

I am running compute_bold_stats on several bolds and the command seems to fail on some of them. As you will see in the log below, octave fails with error -9.

Call:

export STUDY_NAME=“HBN_BBRF_rerun”
export WORK_DIR=“/gpfs/gibbs/pi/aslin/ss2569/Studies”
export RAW_DATA=“${WORK_DIR}/${STUDY_NAME}/sessions/inbox/MR”
export INPUT_BATCH_FILE=“${WORK_DIR}/${STUDY_NAME}/sessions/specs/HBN_BBRF_batch.txt”
export INPUT_MAPPING_FILE=“${WORK_DIR}/${STUDY_NAME}/sessions/specs/HBN_BBRF_mapping.txt”
export SESSIONS=“NDARAA947ZG5”
export RUNTURNKEY_TYPE=“local”
export RUNTURNKEY_STEPS=“compute_bold_stats”

qunex_container run_turnkey
–rawdatainput=“${RAW_DATA}”
–paramfile=“${INPUT_BATCH_FILE}”
–mappingfile=“${INPUT_MAPPING_FILE}”
–workingdir=“${WORK_DIR}”
–projectname=“${STUDY_NAME}”
–path=“${WORK_DIR}/${STUDY_NAME}”
–sessions=“${SESSIONS}”
–sessionids=“${SESSIONS}”
–sessionsfolder=“sessions”
–turnkeytype=“${RUNTURNKEY_TYPE}”
–container=“${QUNEX_CONTAINER}”
–overwrite=“yes”
–turnkeysteps=“${RUNTURNKEY_STEPS}”
–parsessions=“1”
–scheduler=“SLURM,time=23:59:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=day”

Log:

Generated by QuNex 0.94.9 on 2022-10-01_12.05.38.437241

e[36m===> Executing QuNex run_turnkey workflow… e[0m

e[32m------------------------ Initiating QuNex Turnkey Workflow ------------------------------- e[0m

e[35m → Note: Acceptance Test type not specified. Setting default type to: no e[0m

e[35m → Note: Turnkey cleaning not specified. Setting default to: no e[0m

e[32m–> Checking that requested compute_bold_stats are supported… e[0m

e[32m compute_bold_stats is supported. e[0m

e[32m–> Verified list of supported Turnkey steps to be run: compute_bold_stats e[0m

– run_turnkey.sh: Specified Command-Line Options - Start –

QuNex Turnkey run type: local
QuNex Turnkey clean interim files: no
Local project name: HBN_BBRF_rerun
Raw data input path: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/inbox/MR
QuNex Session variable name: NDARAA306NT2
QuNex Parameters file input: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/specs/HBN_BBRF_batch1.txt
QuNex Mapping file input: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/specs/HBN_BBRF_mapping1.txt
QuNex Project-specific final Batch file path: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing
QuNex Study folder: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun
QuNex Log folder: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs
QuNex Session-specific working folder: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/inbox
Overwrite for a given turnkey step set to: yes
Overwrite for session set to: no
Overwrite for project set to: no
Overwrite for the entire XNAT project: no
Cleanup for session set to: no
Cleanup for project set to: no
Custom QC requested:
Sessionids parameter: NDARAA306NT2
Turnkey workflow steps: compute_bold_stats
Acceptance test requested: no

– run_turnkey.sh: Specified Command-Line Options - End –

e[32m------------------------- Starting QuNex Turnkey Workflow -------------------------------- e[0m

e[32m-------------------------------------------------------------- e[0m
e[32m QuNex Environment Status Report e[0m
e[32m-------------------------------------------------------------- e[0m

e[32m OS Version e[0m
e[32m---------------------------------------------- e[0m

           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"

e[32m QuNex General Environment Variables e[0m
e[32m---------------------------------------------- e[0m

             QuNexVer : 0.94.9
                TOOLS : /opt
            QUNEXREPO : qunex
            QUNEXPATH : /opt/qunex
             QUNEXENV : /opt/env/qunex
       TemplateFolder : /opt/qunex/qx_library/data/
        QUNEXMCOMMAND : octave -q --no-init-file --eval

e[32m Core Dependencies Environment Variables e[0m
e[32m---------------------------------------------- e[0m

             CONDADIR : /opt/miniconda
               FSLDIR : /opt/fsl/fsl
           FSLCONFDIR : /opt/fsl/fsl/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

e[32m HCP Pipelines e[0m
e[32m---------------------------------------------- e[0m

           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 : /opt/fsl/fsl/bin/eddy_cuda9.1
ASLDIR : /opt/HCP/HCPpipelines/hcp-asl

e[32m Binary / Executable Locations and Versions e[0m
e[32m---------------------------------------------- e[0m

HCPpipelines TAG : v4.5.0

HCPpipelines commit : 0c0345ff561aaab46ef95ffad7b691ab0222b430

     FSL Binary  : /opt/fsl/fsl/bin/fsl
     FSL Version : 6.0.5.1:57b01774

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: Aug  5 2022 (Version AFNI_22.2.05 'Marcus Aurelius')

    ANTs Binary  : /opt/ANTs/ANTs/bin/antsJointFusion
    ANTs Version : ANTs Version: 2.3.5.dev1-g6f137

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

error: pkg: cannot create file /opt//opt/octave/octavepkg/octave_packages
error: called from
pkg at line 510 column 13
/home/ss2569/.octaverc at line 11 column 1
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  ‘3.3.6’

    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

e[32m Full Environment Paths e[0m
e[32m---------------------------------------------- e[0m

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:/opt/freesurfer/freesurfer-6.0/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:

e[32m=================== QuNex environment set successfully! ==================== e[0m

e[32m --------------------------------------------------------------------- e[0m

e[32m ===> Executing specific QuNex turkey workflow steps: compute_bold_stats e[0m

e[32m --------------------------------------------------------------------- e[0m

e[36m ===> RUNNING run_turnkey step ~~~ compute_bold_stats e[0m

e[32m … Running QuNex v0.94.9 … e[0m

e[36m— Full QuNex call for command: compute_bold_stats e[0m

e[36mgmri compute_bold_stats --sessions=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/HBN_BBRF_batch1.txt” --sessionsfolder=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions” --overwrite=“yes” --logfolder=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs” --sessionids=“NDARAA306NT2” --bolds=“all” e[0m

e[36m--------------------------------------------------------- e[0m

WARNING: passing the batchfile through the sessions parameter will be deprecated, please use the batchfile parameter!
WARNING: the sessionids parameter will be deprecated, please use the sessions parameter!

WARNING: Use of parameters with changed name(s)!
The following parameters have new names:
… hcp_Pipeline is now hcp_pipeline!
… TR is now tr!
Please correct the listed parameter names in command line or batch file!

WARNING: Use of deprecated parameter value(s)!
The following parameter values have changed:
… original (hcp_filename) is now userdefined!
Please correct the listed parameter values in command line or batch file!
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to ‘_Atlas’!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ‘’!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to ‘_Atlas’!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ‘’!

Generated by QuNex 0.94.9 on 2022-10-01_12.05.50.420993

=================================================================
gmri compute_bold_stats
–sessions=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/HBN_BBRF_batch1.txt”
–sessionsfolder=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions”
–overwrite=“yes”
–logfolder=“/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs”
–sessionids=“NDARAA306NT2”
–bolds=“all” \

Starting multiprocessing sessions in /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/HBN_BBRF_batch1.txt with a pool of 1 concurrent processes

---- Running local

Starting processing of sessions NDARAA306NT2 at Saturday, 01. October 2022 12:05:50
Running external command: octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold1.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

You can follow command’s progress in:
/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/tmp_compute_bold_stats_B1_NDARAA306NT2_2022-10-01_12.05.50.444532.log

Running external command: octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold2.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

You can follow command’s progress in:
/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/tmp_compute_bold_stats_B2_NDARAA306NT2_2022-10-01_12.05.50.447476.log

Running external command: octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold3.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

You can follow command’s progress in:
/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/tmp_compute_bold_stats_B3_NDARAA306NT2_2022-10-01_12.06.33.645266.log

Running external command: octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold4.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

You can follow command’s progress in:
/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/tmp_compute_bold_stats_B4_NDARAA306NT2_2022-10-01_12.07.37.786498.log


Session id: NDARAA306NT2
[started on Saturday, 01. October 2022 12:05:50]

Computing BOLD image statistics …

Files in 'images/functional will be processed.

The command will compute per frame statistics for each of the specified BOLD
files based on its movement correction parameter file and BOLD image analysis.
The results will be saved as *.bstat and *.bscrub files in the images/movement
subfolder. Only images specified using --bolds parameter will be
processed (see documentation). Do also note that even if cifti is specifed as
target format, nifti volume image will be used to compute statistics.

Using parameters:

--mov_radius: 50.0
--mov_fd: 0.5
--mov_dvars: 3.0
--mov_dvarsme: 1.6
--mov_after: 0
--mov_before: 0
--mov_bad: udvarsme

for computing scrubbing information.

Working on BOLD images in: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional
Resulting files will be in: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement

Based on the settings, all BOLD files will be processed (see --bolds).
If already present, existing statistics will be overwritten (see --overwrite).
Processing 2 BOLDs in parallel

Working on: bold1 …
… checking for data
… movement data present [bold1_mov.dat]
… bold data present [bold1.nii.gz]

Working on: bold1 …
… checking for data
… movement data present [bold1_mov.dat]
… bold data present [bold1.nii.gz]

… running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold1.nii.gz

ERROR: … running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold1.nii.gz failed with error -9

command executed:
octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold1.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

—> logfile: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/error_compute_bold_stats_B1_NDARAA306NT2_2022-10-01_12.05.50.444532.log

Working on: bold2 …
… checking for data
… movement data present [bold2_mov.dat]
… bold data present [bold2.nii.gz]

… running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold2.nii.gz
—> compute_bold_stats test file [bold2.bstats] present
—> logfile: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/done_compute_bold_stats_B2_NDARAA306NT2_2022-10-01_12.05.50.447476.log

Working on: bold3 …
… checking for data
… movement data present [bold3_mov.dat]
… bold data present [bold3.nii.gz]

… running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold3.nii.gz
—> compute_bold_stats test file [bold3.bstats] present
—> logfile: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/done_compute_bold_stats_B3_NDARAA306NT2_2022-10-01_12.06.33.645266.log

Working on: bold4 …
… checking for data
… movement data present [bold4_mov.dat]
… bold data present [bold4.nii.gz]

Working on: bold4 …
… checking for data
… movement data present [bold4_mov.dat]
… bold data present [bold4.nii.gz]

… running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold4.nii.gz

ERROR: … running matlab general_compute_bold_stats on /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold4.nii.gz failed with error -9

command executed:
octave -q --no-init-file --eval “try general_compute_bold_stats(‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/bold4.nii.gz’, ‘’, ‘/gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/sessions/NDARAA306NT2/images/functional/movement’, ‘same’, ‘radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme’, true); catch ME, general_report_crash(ME); exit(1), end; exit”

—> logfile: /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/error_compute_bold_stats_B4_NDARAA306NT2_2022-10-01_12.07.37.786498.log

Bold statistics computation completed on Saturday, 01. October 2022 12:07:58

===> Final report for command compute_bold_stats
… NDARAA306NT2 —> BOLDS done: 0, missing data: 0, failed: 2, processed: 2, skipped: 0
===> Not all tasks completed fully!

e[32m------------------------- Successful completion of work -------------------------------- e[0m

Alonso, hi!

Would it be possible to attach the two error log files:

  • /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/error_compute_bold_stats_B1_NDARAA306NT2_2022-10-01_12.05.50.444532.log
  • /gpfs/gibbs/pi/aslin/ss2569/Studies/HBN_BBRF_rerun/processing/logs/comlogs/error_compute_bold_stats_B4_NDARAA306NT2_2022-10-01_12.07.37.786498.log

They should have the information on why the functions failed. It seems you are running these analyses on the Yale Grace cluster. If you can grant access to the relevant study folder to my username (or28), I could inspect the logs and files directly and help you more efficiently.

With kind regards, Grega

Hi Alonso,

Is there anything new regarding this issue? Can we close it?

Cheers, Jure