[RESOLVED] How to specify parameters for qunex commands when using turnkey

Dear Jure and QuNex experts:

Apologies for this very basic question. I was wondering how to specify the parameters for qunex commands (e.g. in this case dwi_dtifit) when using turnkey?

I have either tried putting the parameters inside a batch file (${INPUT_BATCH_FILE}) but it did not work as expected.
qunex_container run_turnkey --rawdatainput="${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="${RUNTURNKEY_TYPE}" --nv --container="${QUNEX_CONTAINER}" --turnkeysteps="${RUNTURNKEY_STEPS}" --overwrite="yes"

I have also tried to specify it like the following but also did not work
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}" --nv --container="${QUNEX_CONTAINER}" --turnkeysteps="${RUNTURNKEY_STEPS}" --kurt="yes" --overwrite="yes"

Please kindly advise, and your help would be greatly appreciated as always!

Many thanks,
Ed

Hi Ed,

There are several ways to specify parameters through the run_turnkey command, either by using a batch file, or by specifying additional parameters to the run_turnkey command. However, the second option only works for a very limited subset of options, and unfortunately kurt is not one of them, nor do any of the dwi_dtifit parameters. Similarly only a subset of all the parameters are supported by the parameters file, which can be found in the example batch parameters file. The easiest way right now is to call dwi_dtifit directly without using run_turnkey. The command should look like this.

qunex_container dwi_dtifit \
  --sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
  --sessions="${SESSIONS}" \
  --overwrite="yes" \
  --kurt="yes" \
  --container="${QUNEX_CONTAINER}"

Lining

Hi Lining:

Thanks so much for your help! It works nicely.

Best,
Ed