Dear Jure and QuNex experts:
I was trying to run hcp_diffusion (and all other HCP preprocessing pipelines) using qunex_container. However, it returned with error (error_hcp_diffusion_001B_2022-08-18_07.18.22.077156.log (52.6 KB)
see attached). It appeared that eddy_cuda would not run. Please find below my script for calling the qunex container for your reference:
PATH=${HOME}/qunex:${PATH}
export STUDY_NAME="cimt"
export WORK_DIR="${HOME}/qunex"
export QUNEX_CONTAINER="${WORK_DIR}/qunexcontainer/qunex_suite-0.93.6.sif"
export RAW_DATA="${WORK_DIR}/data"
export INPUT_BATCH_FILE="${RAW_DATA}/006_batch.txt"
export INPUT_MAPPING_FILE="${RAW_DATA}/006_mapping.txt"
export SESSIONS="001A,001B,001C,001D,002A,002B,002C,003A,003B,003C,003D,004A,004B,004C,006A,006C"
export RUNTURNKEY_TYPE="local"
export RUNTURNKEY_STEPS="create_study,map_raw_data,import_dicom,create_session_info,setup_hcp,create_batch,hcp_pre_freesurfer,hcp_freesurfer,hcp_post_freesurfer,hcp_fmri_volume,hcp_fmri_surface,hcp_diffusion,map_hcp_data,create_bold_brain_masks,compute_bold_stats,create_stats_report,extract_nuisance_signal,preprocess_bold"
qunex_container run_turnkey --rawdatainput="${RAW_DATA}" --batchfile="${INPUT_BATCH_FILE}" --mappingfile="${INPUT_MAPPING_FILE}" --workingdir="${WORK_DIR}" --projectname="${STUDY_NAME}" --path="${WORK_DIR}/${STUDY_NAME}" --sessions="${SESSIONS}" --sessionids="${SESSIONS}" --sessionsfoldername="sessions" --turnkeytype="${RUNTURNKEY_TYPE}" --container="${QUNEX_CONTAINER}" --turnkeysteps="${RUNTURNKEY_STEPS}" --overwrite="yes"
However when I tried to run the exact same eddy_cuda command from terminal, eddy_cuda successfully ran. So I was wondering if you could kindly tell me what was the root cause of this?
Any help would be greatly appreciated.
Many thanks,
Edward