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

Use Questions
1

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

2

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

3

Hi Lining:

Thanks so much for your help! It works nicely.

Best,
Ed

4

Hi Lining:

I ran into problem again with dwi_dtifit (via qunex_container) when I added --kurtdir and --save_tensor, none of the associated maps were computed. I checked the log file and it seems that the command that was called inside dwi_dtifti did not have any of the above flags in it.

Please kindly advise.

Many thanks,
Ed

5

Hi Ed,

Unfortunately, run_turnkey supports only a subset of parameters. We are developing a new run_turnkey engine that will be much more user friendly and efficient. However, it is still far away from being released to the public. I would advise you to use dwi_dtifit command separately and not through run_turnkey if possible.

Jure

6

Hi Jure:

I did run the dwi_dtifit separately using the command below:

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

But looks like the --kurtdir and --save_tensor were not executed.

Many thanks!
Ed

7

Ed, and save_tensor was used? Please try

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

Thanks!

8

Hi Jure:

I have just tried and looks like those two flags were ignored again.

Please kindly advise.

Many thanks,
Ed

9

Hi,

I will try to reproduce this tomorrow on our end. Could you upload the comlog and the runlog that get created with your call. Thanks!

Jure

10

Never mind, I had some time and I was able to recreate this. I think I found the bug. Will fix it with the next release. If this is something supper pressing, I can try to find a workaround.

Jure

11

Hi Jure:

Sorry for my late reply because of the time zone difference;)

Glad to know that this can be fixed!

Many thanks for taking the time!

Best,
Ed