[RESOLVED] Parcellate_bold fails to run

ehui · September 8, 2022, 3:21am

Dear QuNex Experts:

I was trying to run parcellate_bold to obtain the functional connectome with the following commands:

qunex_container parcellate_bold \
  --sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
  --sessions="${SESSIONS}" \
  --inputfiles="bold1_Atlas.dtseries.nii" \
  --inputpath="/images/functional" \
  --parcellationfile="${HOME}/projects/Pipeline/global/templates/ColeAnticevicNetPartition/CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dlabel.nii" \
  --mask="" \
  --computepconn="yes" \
  --outname="ColeAnticevicNetPartition" \
  --outpath="/images/functional" \
  --inputdatatype="dtseries" \
  --overwrite="yes" \
  --container="${QUNEX_CONTAINER}"

However, the following errors occurred:

NOTE: Weights file not used.
ERROR: Input file value missing

I had no idea what went wrong. Any help would be greatly appreciated. Thank you very much.

Best,
Ed

liningpan · September 8, 2022, 1:29pm

Hi Ed,

I believe there is a typo in the documentation. For parcellate_bold, the parameter should be inputfile instead of inputfiles (for compute_bold_fc the parameter is inputfiles). I will fix the documentation shortly. Sorry about this!

Lining

ehui · September 9, 2022, 2:23pm

Dear Lining:

Many thanks for your swift help indeed;)

Best,
Ed

ehui · September 13, 2022, 6:33am

Dear Lining:

Can you be so kind to let me know how to fix the error please?

ERROR: Study folder or sessions folder is not defined or missing.
       Check your inputs and re-run QuNex.

Below is the command I used:

qunex_container parcellate_bold \
  --sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
  --sessions="${SESSIONS}" \
  --inputfile="bold1_Atlas_s_hpss_res-mVWMWB_lpss.dtseries.nii,bold2_Atlas_s_hpss_res-mVWMWB_lpss.dtseries.nii" \
  --inputpath="/images/functional/" \
  --parcellationfile="${HOME}/projects/Pipeline/global/templates/ColeAnticevicNetPartition/CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dlabel.nii" \
  --mask="" \
  --computepconn="yes" \
  --outname="ColeAnticevicNetPartition" \
  --outpath="/images/functional/" \
  --inputdatatype="dtseries" \
  --overwrite="yes" \
  --container="${QUNEX_CONTAINER}"

Thanks so much for your help in advance!

Best,
Ed

liningpan · September 13, 2022, 2:37pm

Hi Ed,

First of all, I don’t think parcellate_bold accepts multiple input files. For this error, could you please double check that your environment variables such as WORK_DIR and STUDY_NAME are defined? I would also be helpful if you can share the complete log with us.

Lining

ehui · September 13, 2022, 3:16pm

Hi Lining:

The same error occurred even after I specified only one input file.

Kindly note that the environmental variables WORK_DIR and STUDY_NAME were defined. And for some reason, I couldn’t find any log file associated with parcellate_bold from the “${WORK_DIR}/${STUDY_NAME}/processing/logs/comlogs”.

Many thanks for your help!

Best,
Ed

liningpan · September 13, 2022, 4:26pm

If there’s no comlogs, can you share more complete logs printed into the terminal?

ehui · September 13, 2022, 4:44pm

Hi Lining:

Actually that was pretty much it:

Generated by QuNex
------------------------------------------------------------------------
Version: 0.93.6
User: ehui
System: ehui
OS: RedHat Linux #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022
------------------------------------------------------------------------

        ██████\                  ║      ██\   ██\
       ██  __██\                 ║      ███\  ██ |
       ██ /  ██ |██\   ██\       ║      ████\ ██ | ██████\ ██\   ██\
       ██ |  ██ |██ |  ██ |      ║      ██ ██\██ |██  __██\\██\ ██  |
       ██ |  ██ |██ |  ██ |      ║      ██ \████ |████████ |\████  /
       ██ ██\██ |██ |  ██ |      ║      ██ |\███ |██   ____|██  ██\
       \██████ / \██████  |      ║      ██ | \██ |\███████\██  /\██\
        \___███\  \______/       ║      \__|  \__| \_______\__/  \__|
            \___|                ║


                       DEVELOPED & MAINTAINED BY:

                    Anticevic Lab, Yale University
               Mind & Brain Lab, University of Ljubljana
                     Murray Lab, Yale University

                      COPYRIGHT & LICENSE NOTICE:

Use of this software is subject to the terms and conditions defined in
'LICENSE.md' which is a part of the QuNex Suite source code package:
https://bitbucket.org/oriadev/qunex/src/master/LICENSE.md

 ---> Setting up Octave


 ........................ Running QuNex v0.93.6 ........................




ERROR: Study folder or sessions folder is not defined or missing.
       Check your inputs and re-run QuNex.

Many thanks!
Ed

liningpan · September 13, 2022, 5:11pm

Do you see any scripts in the processing/logs/batchlogs folder or your home folder?

ehui · September 13, 2022, 5:22pm

No, the folder is empty. Thanks, Ed

liningpan · September 13, 2022, 6:31pm

Whenever you run something through qunex_container, it will always generate a script before running either in you home folder or the batchlogs folder. The name of the script will be something like qunex_container_command_[timestamp].sh

ehui · September 14, 2022, 12:27am

Hi Lining:

Weirdly there isn’t any script in any folders after running parcellate_bold. However, I did get log files in processing/logs/comlogs when I ran e.g. dwi_parcellate through qunex_container.

Many thanks,
Edward

liningpan · September 14, 2022, 1:02pm

Could you please try again with the latest qunex_container script? QuNex quick start using a Docker container — QuNex documentation

ehui · September 16, 2022, 6:54am

Hi Lining:

Apologies for my late response. I stumbled on the root cause of the problem. I have moved all the data to another drive which only has read access. Once I moved it to ${home} directory, all is working normal.

On the topic of drive with only read access. I have changed it to write/read but the entire qunex_container script wouldn’t run and complained the file system is a read only system. May I ask if you have come across such issue before?

Many thanks for your help as always!

Best,
Ed

liningpan · September 16, 2022, 3:36pm

Something we usually encounter when moving study folders around is absolute paths in session.txt, session_hcp.txt, and batch files.

Also for singularity containers you also want to make sure that the data folders are mounted and have rw permission.

https://qunex.readthedocs.io/en/latest/wiki/UsageDocs/RunningQunexContainer.html?highlight=bind#binding-mapping-external-folders-or-setting-additional-container-parameters

https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#user-defined-bind-paths