Description:
Hi Qunex team, thank you for all your hardword for developing and maintaining this framework. I am currently following the Quickstart guideline to toy the software. I got the following error when the process coming into the PreFresurfer process. I already attached the command and the log that I got after I ran the command. Thank you for any help and support.
Call:
qunex_container run_recipe --recipe_file="${RAW_DATA}/recipe.yaml" --recipe="quick_start" --bash_post="${BASH_POST}" --bind="${HOME}:${HOME}" --container="${QUNEX_CONTAINER --overwrite="yes"
Logs:
============================== RUN_RECIPE LOG ==============================
---> Running commands from recipe: quick_start
---> Commands:
- create_study
- import_dicom
- create_session_info
- setup_hcp
- create_batch
- hcp_pre_freesurfer
- hcp_freesurfer
- hcp_post_freesurfer
- hcp_fmri_volume
- hcp_fmri_surface
--------------------------------------------
---> Running command:
qunex create_study \
--studyfolder='/home/vhluong/qunex/quickstart'
--------------------------------------------
---> Running command:
qunex import_dicom \
--masterinbox='/home/vhluong/qunex/data' \
--archive='leave' \
--overwrite='yes' \
--sessionsfolder='/home/vhluong/qunex/quickstart/sessions' \
--sessions='HCPA001'
Final report
============
Successfully processed:
... HCPA001 [/home/vhluong/qunex/data/HCPA001.zip]
-----------------------------------------
Finished at 2025-09-20 03:49:06
---> Successful completion of task
--------------------------------------------
---> Running command:
qunex create_session_info \
--mapping='/home/vhluong/qunex/data/HCPA001_mapping.txt' \
--overwrite='yes' \
--sessionsfolder='/home/vhluong/qunex/quickstart/sessions' \
--sessions='HCPA001'
---> Final report
---> sessions with processed file:
-> HCPA001
-----------------------------------------
Finished at 2025-09-20 03:49:07
---> Successful completion of task
--------------------------------------------
---> Running command:
qunex setup_hcp \
--sourcefolder='/home/vhluong/qunex/quickstart/sessions/HCPA001' \
--sessionsfolder='/home/vhluong/qunex/quickstart/sessions' \
--sessions='HCPA001' \
--batchfile='/home/vhluong/qunex/quickstart/processing/batch.txt'
---> Final report for command setup_hcp
... setup_hcp: HCPA001 completed
---> Successful completion of task
--------------------------------------------
---> Running command:
qunex create_batch \
--targetfile='/home/vhluong/qunex/quickstart/processing/batch.txt' \
--paramfile='/home/vhluong/qunex/data/HCPA001_parameters.txt' \
--overwrite='yes' \
--sessionsfolder='/home/vhluong/qunex/quickstart/sessions' \
--sessions='HCPA001'
--------------------------------------------
---> Running command:
qunex hcp_pre_freesurfer \
--overwrite='yes' \
--studyfolder='/home/vhluong/qunex/quickstart' \
--sessionsfolder='/home/vhluong/qunex/quickstart/sessions' \
--sessions='HCPA001' \
--batchfile='/home/vhluong/qunex/quickstart/processing/batch.txt'
ERROR: Unknown error occured:
...................................
Traceback (most recent call last):
File "/opt/env/qunex/lib/python3.12/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'NONE'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 1309, in hcp_pre_freesurfer
resolution, res_report = _set_hcp_prefs_template_res(t1w)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 1560, in _set_hcp_prefs_template_res
img = nib.load(image)
^^^^^^^^^^^^^^^
File "/opt/env/qunex/lib/python3.12/site-packages/nibabel/loadsave.py", line 44, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'NONE'
...................................
HCP PreFS completed on Saturday, 20. September 2025 03:49:10
------------------------------------------------------------
---> Final report for command hcp_pre_freesurfer
... HCPA001 ---> PreFS failed
---> Not all tasks completed fully!
----==== RECIPE EXECUTION SUMMARY ====----
Recipe: quick_start
- command create_study ... OK
- command import_dicom ... OK
- command create_session_info ... OK
- command setup_hcp ... OK
- command create_batch ... OK
- command hcp_pre_freesurfer ... FAILED
----------==== END SUMMARY ====----------
---> run_recipe not completed successfully: failed running command hcp_pre_freesurfer
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