Description:
When running hcp_diffusion via turnkey, I got this ‘ERROR: echo-spacing not specified’ despite the parameter being specified in parameter file (attached) in “_hcp_dwi_echospacing” qunex parameter. All other parameters are specified correctly, only “–echospacing” parameter is missing. See:
/opt/HCP/HCPpipelines/DiffusionPreprocessing/DiffPreprocPipeline.sh
–path=“/storage/brno2/home/pe_so/qunex/quickstart/sessions/original/hcp”
–subject=“original”
–PEdir=2
–posData=“/storage/brno2/home/pe_so/qunex/quickstart/sessions/original/hcp/original/unprocessed/Diffusion/original_DWI_dir30_PA.nii.gz”
–negData=“/storage/brno2/home/pe_so/qunex/quickstart/sessions/original/hcp/original/unprocessed/Diffusion/original_DWI_dir30_AP.nii.gz”
–echospacing=“”
–gdcoeffs=“NONE”
–dof=“6”
–b0maxbval=“50”
–combine-data-flag=“1”
–printcom=“”
When I ran the hcp_diffusion command directly I got an error copied bellow.
Call:
- via turnkey:
qunex_container run_turnkey
–rawdatainput=“/data”
–dataformat=“DICOM”
–paramfile=“${INPUT_BATCH_FILE}”
–mappingfile=“${INPUT_MAPPING_FILE}”
–workingdir=“${WORK_DIR}”
–projectname=“${STUDY_NAME}”
–path=“${WORK_DIR}/${STUDY_NAME}”
–sessionsfoldername=“sessions”
–sessions=“${SESSIONS_LIST}”
–batchfile=“${WORK_DIR}/batch.txt”
–turnkeytype=“${RUNTURNKEY_TYPE}”
–container=“${HOME}/qunex/qunex_suite-0.93.6.sif”
–turnkeysteps=“${RUNTURNKEY_STEPS}”
–bind=“${RAW_DATA}:/data” \
- directly:
qunex_container hcp_diffusion
–batchfile=“/storage/brno2/home/pe_so/qunex/quickstart/processing/batch.txt”
–sessionsfolder=“/storage/brno2/home/pe_so/qunex/quickstart/sessions”
–sessions=“original”
–overwrite=“no”
–parsessions=“1”
–hcp_dwi_echospacing=“0.98”
–hcp_dwi_combinedata=“1”
–hcp_dwi_nogpu
–container=“/storage/brno2/home/pe_so/qunex/qunex_suite-0.93.6.sif”
Logs: when hcp_diffusion ran directly not via turnkey
Generated by QuNex 0.93.6 on 2022-08-10_18.03.32.972711
=================================================================
gmri hcp_diffusion
–sessionsfolder=“/storage/brno2/home/pe_so/qunex/quickstart/sessions”
–parsessions=“1”
–hcp_dwi_echospacing=“0.98”
–hcp_dwi_combinedata=“1”
–hcp_dwi_nogpu=“True”
–batchfile=“/storage/brno2/home/pe_so/qunex/quickstart/processing/batch.txt”
–sessions=“original” \
Starting multiprocessing sessions in original with a pool of 1 concurrent processes
---- Running local
Starting processing of sessions original at Wednesday, 10. August 2022 18:03:32
Session id: original
[started on Wednesday, 10. August 2022 18:03:32]
Running HCP DiffusionPreprocessing Pipeline [HCPStyleData] …
ERROR: Unknown error occured:
…
Traceback (most recent call last):
File “/opt/qunex/python/qx_utilities/hcp/process_hcp.py”, line 2161, in hcp_diffusion
hcp = getHCPPaths(sinfo, options)
File “/opt/qunex/python/qx_utilities/hcp/process_hcp.py”, line 114, in getHCPPaths
hcpbase = os.path.join(sinfo[‘hcp’], sinfo[‘id’] + options[‘hcp_suffix’])
KeyError: ‘hcp’
…
Many thanks for help.
Best,
Petr
dwi_parameters.txt (2.7 KB)
