[RESOLVED] Run_list command error

Issues
1

Hi everyone.

I’m having some issues with the run_list command.
I have a certain number of subjects (BIDS format) and I’d like to set a list of commands to do for each one (with parsession to save some computational time).

I’ve seen from the qunex wiki that the run_list command is what I was looking for. I’ve created the study folder and I’ve written a runlist.txt (and saved it in data input folder) file following the example:

global settings

sessionsfolder : /output/mystudy/sessions
overwrite : yes
sessions : 0*

list: dataImport

command: import_bids
    inbox   : /input
    archive : leave

list: prepareHCP

command: create_session_info

command: create_batch
    targetfile : /output/mystudy/processing/batch_hcp.txt

command: setup_hcp

list: doHCP

sessions    : /output/mystudy/processing/batch_hcp.txt
parsessions : 4

command: hcp_pre_freesurfer

command: hcp_freesurfer

command: hcp_post_freesurfer

command: hcp_fmri_volume
    parsessions : 4
    parelements : 4

command: hcp_fmri_surface
    parsessions : 4
    parelements : 4

Unfortunately after using the command:

qunex run_list \
- -listfile=“/input/runlist.txt” \
- -runlists=“dataImport”

I obtain the following error message:

… Running QuNex v0.90.6 …

---> Resetting to defaults:

— Full QuNex call for command: run_list

gmri run_list --listfile=“/input/runlist.txt” --runlists=“dataImport”

===> Saving the run_list runlog to: /opt/qunex/runlogs
===> Running commands from the following lists: dataImport
===> Running commands from list: dataImport

--------------------==== QuNex failed! ====--------------------

ERROR: Execution of command run_list failed!
Please check documentation for the command (qunex ?run_list)!

The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)

qunex run_list
–listfile=/input/runlist.txt
–runlists=dataImport

Here’s the error as caught by python:

Traceback (most recent call last):
File “/opt/qunex/python/qx_utilities/gmri”, line 499, in
main()
File “/opt/qunex/python/qx_utilities/gmri”, line 467, in main
runCommand(comm, opts)
File “/opt/qunex/python/qx_utilities/gmri”, line 275, in runCommand
gcom.commands[command]‘com’
File “/opt/qunex/python/qx_utilities/general/utilities.py”, line 1820, in run_list
if commandName in commands.commands:
NameError: global name ‘commands’ is not defined

If anyone can give me some advice on how to solve this it will be very helpful.

Best regards,
Chiara

2

Hi Chiara,

Thanks for reporting this. The run_list command is still in development and not yet fully tested and debugged. Our goal is to integrate the run_list functionality into run_turnkey and have a single, powerful command for executing a sequence of QuNex commands (either through providing processing steps or by creating a command’s list). However, we currently have some urgent development on our hands, because of this run_list finalization is not on top of our ToDo list and I cannot give you an estimated release date for this functionality.

To avoid confusion I added a short disclaimer to the top of run_list's Wiki page saying

Disclaimer

This functionality is still in development and not yet fully tested and debugged. For the time being we recommend users to process their data with other QuNex approaches. Obviously, you are free to play around and test this, if you do so, please let us know of any bugs you encounter.

Sorry for not making this clear on our Wiki before and thank you again for reporting the bugs. The reported bug will be removed in the next release QuNex version but like I said, do not expect run_list to be “bulletproof” at that point in time.

Thanks, Jure

1 Like
3

Hi Jure,

Thank you for your answer. No problem, I’ll try another approach then.

Best Regards,
Chiara