[RESOLVED] Error in hcp_msmall-name 'session' is not defined

Use Questions
1

Hi,
I encountered an error while using the hcp_msmall function, and I’m not sure what caused it. I’d like to get some help.

Here is my hcp_msmall command.
hcp_msmall)
# --hcp_icafix_highpass=“2000”
# --hcp_highresmesh=“164”
qunex_container hcp_msmall
–sessionsfolder=“${WORK_DIR}/${STUDY_NAME}/sessions”
–batchfile=“${WORK_DIR}/${STUDY_NAME}/processing/batch.txt”
–hcp_icafix_bolds=“rest”
–bind=“${SDIR}:${SDIR}” \
–container=“${QUNEX_CONTAINER}”;
;;

Here is my ‘log’ file"
try_step15.log (6.4 KB)

Best,
Keely

2

Hi Keeley,

Welcom to the QuNex forum!

I already fixed this bug a couple of days ago, a new QuNex version will be released in a week or so.

Based on the log you are not denoising your data optimally. It seems like you used the old/legacy version of HCP ICAFix called Single Run ICAFix. This version exists only for backwards compatibility if you want to redo some work on older studies. When processing new data, you shuld be using Multi Run ICAFix. Which one gets used is determined by the hcp_icafix_bolds parameters. If you specify group:<list_of_bolds> then Multi Run ICAFix will be used, if you specify only <list_of_bolds> then the old/deprecated Single Run ICAFix will be used, which happened in your case. See our documentation for additional details.

If your data has only resting state data, or if you want to denoise all BOLDs, do not set this parameter and the default setting will automatically set it appropriately for a Multi Run HCP ICAFix run.

Best, Jure

4

Hi Jure,
Thank you for your help. hcp_msmall can run normally now, but I have encountered a new problem. In the run_qc_bold step, please help me look at the log file with errors and how to solve this problem. Because this is my first time processing MRI data, I don’t know enough about the overall structure of the data, so I don’t know where to start to solve this error. Thank you very much for your help.
Here is my command
run_qc_bold)
qunex_container run_qc
–sessionsfolder=“${WORK_DIR}/${STUDY_NAME}/sessions”
–batchfile=“${WORK_DIR}/${STUDY_NAME}/processing/batch.txt”
–sessions=“${SUBJ}”
–modality=“BOLD”
–boldprefix=“BOLD”
–boldsuffix=“Atlas”
–bind=“${SDIR}:${SDIR}”
–container=“${QUNEX_CONTAINER}”;
;;
Here is my ‘log’ file
try_step21.log (378.0 KB)

Best,
Keely

5

Hi,

Does run_qc work for other modalities (e.g., T1w, T2w …)? Try running a simple T1w QC first and see if it works.

Can you try running this:

qunex_container run_qc \
  --sessionsfolder="/mnt/ssd2/qzheng/Project2_stroke_recovery/qunex/try/sessions" \
  --batchfile="/mnt/ssd2/qzheng/Project2_stroke_recovery/qunex/try/processing/batch.txt" \
  --sessions="${SUBJ}" \
  --modality="BOLD" \
  --boldsuffix="Atlas" \
  --bind="/mnt/ssd2/qzheng:/mnt/ssd2/qzheng" \
  --container="${QUNEX_CONTAINER}"

Some general pointers about issues reporting. Please encapsulate command calls or code examples in triple back ticks, so start the block with a triple back tick and end it the same way. That way it will look my call above and not like yours.

QuNex generates logs in /mnt/ssd2/qzheng/Project2_stroke_recovery/qunex/try/processing/logs/runlogs and /mnt/ssd2/qzheng/Project2_stroke_recovery/qunex/try/processing/logs/comlogs. Every command call will generate logs there, please upload those files and not your console printout. That way it is much easier for me to help you.

Best, Jure

6

Hi Jure,
run_qc can now run the result, but although it ran successfully, there is still an “openGL error” in the log file. Can I ignore this error when using this function in the future? Attached are my runlogs and comlogs.
Log-run_qc_bold_001A_2025-07-08_07.28.11.361042.log (942 Bytes)
done_run_qc_bold_001A_2025-07-08_07.28.11.361042.log (75.0 KB)

Best,
Keely

7

Hi, this is just an issue with some font rendering. If the QC PNGs are generated and they are readable then you can ignore this.

Best, Jure