[RESOLVED] MSMAll bold parsing issue

Issues
1

Hey Jure,

It seems I am running into a bold parsing issue during MSMAll when using version 1.1.1 (and the latest version of the qunex_container script). Though I am not sure if this is an issue with my hcp_msmall_bolds parameter or if it is a bug, but I thought I would report it here. I can get around it when using 1.0.3 (1.1.0 has the same error).

Thanks again!

Deniz

Logs:

# Generated by QuNex 1.1.1 [QIO] on 2025-04-08_18.23.56.842469
#


============================= LOG ================================

# Generated by QuNex 1.1.1 [QIO] on 2025-04-08_18.23.56.783338#
=================================================================
qunex hcp_msmall \
  --sessionsfolder="/home1/deniz/Datasets/VP00211_HCP/sessions" \
  --hcp_filename="userdefined" \
  --hcp_icafix_bolds="REST:rfMRI_REST_AP,rfMRI_REST_PA|TASK:tfMRI_PVT_RUN1_AP,tfMRI_PVT_RUN2_AP,tfMRI_PVT_RUN3_AP,tfMRI_PVT_RUN4_AP" \
  --hcp_msmall_bolds="rfMRI_REST_AP,rfMRI_REST_PA" \
  --overwrite="yes" \
  --sessions="/home1/deniz/Datasets/VP00211_HCP/processing/VP00211_3T_Prisma_HCP_batch.txt" \
  --sessionids="R0205_3TSESS1" \
=================================================================

Starting multiprocessing sessions in /home1/deniz/Datasets/VP00211_HCP/processing/VP00211_3T_Prisma_HCP_batch.txt with a pool of 1 concurrent processes


------------------------------------------------------------
Session id: R0205_3TSESS1 
[started on Tuesday, 08. April 2025 18:23:56]
Running HCP MSMAll pipeline [HCPStyleData] ...
ERROR: Unknown error occured: 
...................................
Traceback (most recent call last):
  File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 8907, in hcp_msmall
    singleRun, msmallGroup, pars_ok, r = parse_msmall_bolds(options, bolds, r)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 8677, in parse_msmall_bolds
    if mb == b[1] or mb == b[2]:
             ~^^^
KeyError: 1
...................................


HCP MSMAll completed on Tuesday, 08. April 2025 18:23:56
------------------------------------------------------------


---> Final report for command hcp_msmall
... R0205_3TSESS1 ---> HCP MSMAll failed
---> Success status not reported for some or all tasks
2

Hi Deniz,

Yes, seems like a bug. Let me fix this for 1.1.2, glad we have a workaround. In terms of hcp_msmall results from 1.0.3 and 1.1.1, tjhey the same, so you can safely swap.

Could you please upload your batch.txt (/home1/deniz/Datasets/VP00211_HCP/processing/VP00211_3T_Prisma_HCP_batch.txt). Thiw way I can test this on the same use case as you just described. Thanks!

Best, Jure

3

I fixed this and will release it in the scope of 1.1.2.

Best, Jure

4

Apologies for the late reply, Jure. Thanks a lot for fixing this! Best, Deniz