Human Connectome - Development Data Release Inquiry
Bigelow, Jasmine
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Elam, Jennifer
Best,
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org
Sent: Thursday, July 25, 2024 11:01 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: [hcp-users] Human Connectome - Development Data Release Inquiry
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J. A. Quent
Hello everyone,
I apologise if the problem is too trivial but I simply to not find any information in the error message that helps me. I've attached the whole log. Please let me know if you need more information to help me.
What I am trying to do: I am submitting a Level 1 analysis with two runs and for most subjects the GLM finishes without an issue but for this participants doesn't run at all. I am using Qunex - Version 0.95.2 to submit this job:
python3 $path_2_qunex_container_script/qunex_container hcp_task_fmri_analysis \
--sessionsfolder="${data_folder}/sessions/" \
--sessions="${data_folder}/processing/sessions_hcp_batch.txt" \
--sessionids="${sessionids}" \
--overwrite="yes" \
--bash_pre="module load singularity" \
--bind="/public/home2/VNLab/" \
--hcp_task_summaryname="${jobname}" \
--hcp_task_lvl1tasks="${level1_run1_folder}@${level1_run2_folder}" \
--hcp_task_lvl1fsfs="${level1_run1_fsf}@${level1_run2_fsf}" \
--hcp_task_highpass="${filtering}" \
--hcp_bold_final_smoothFWHM="${smoothing}" \
--hcp_task_procstring="MSMAll_hp0_clean" \
--container=$qunex_container_file \
--scheduler="SLURM,mem-per-cpu=${memory},time=${time}, partition=blade, jobname=${jobname},mail-user=${email}, mail-type=ALL, exclude=bnode05"
Here is the beginning of the error message:
triplets found in ../EVs/trial_16.txt
Fri Jul 26 10:32:40 CST 2024:TaskfMRILevel1.sh: While running '/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh R0142_7TSESS1 /home1/Jaquent/Datasets/VP00157_HCP/sessions/R0142_7TSESS1/hcp/R0142_7TSESS1/MNINonLinear/Results /home1/Jaquent/Datasets/VP00157_HCP/sessions/R0142_7TSESS1/hcp/R0142_7TSESS1/MNINonLinear/ROIs /home1/Jaquent/Datasets/VP00157_HCP/sessions/R0142_7TSESS1/hcp/R0142_7TSESS1/MNINonLinear/fsaverage_LR32k tfMRI_OLMe_RUN1_AP tfMRI_OLMe_RUN1_AP_Trial_RSA1_smo4_MSMAll 32 2 2 NONE 2 200 NO NONE NONE NONE MSMAll_hp0_clean NONE':
Fri Jul 26 10:32:40 CST 2024:TaskfMRILevel1.sh: ERROR: 'feat_model' command failed with return code: 1
Fri Jul 26 10:32:40 CST 2024:TaskfMRILevel1.sh: ERROR: 'feat_model' command failed with return code: 1
There isn't really much in the error message (unless I miss something) the only think is that oddly mentions "../EVs/trial_16.txt", which looks fine if I open it, so I still have no idea what's going on.
Please also let me know if you think that's a Qunex issue and not an HCP issue.
Best wishes,
Alex
____________________________________ Jörn Alexander Quent, PhD Post doctoral researcher Fudan University, Shanghai China Institute of Science and Technology for Brain-inspired Intelligence (ISTBI) https://jaquent.me https://twitter.com/J_A_Quent https://istbi.fudan.edu.cn Note: If I e-mail you during a time period that coincides with a period where you’re on leave or that is a holiday period in your region, please do not feel obliged to respond to me before you come back. In a global world people do not celebrate the same holidays.
Glasser, Matthew
This looks like the relevant part of the error message:
No valid
[onset duration strength]
triplets found in ../EVs/trial_16.txt
So you should probably show us what is in that file.
Matt.
From: "'J. A. Quent' via HCP-Users" <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Friday, July 26, 2024 at 4:18 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
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Bigelow, Jasmine
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Sent: Thursday, July 25, 2024 12:01 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Human Connectome - Development Data Release Inquiry
Elam, Jennifer
We are working through the steps of releasing HCP-Development and HCP-Aging Lifespan 3.0 data on NDA that will include the longitudinal timepoints for a subset of subjects. We are hoping that the release will be public by sometime in September. Look for an announcement on this list.
Best,
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org
Sent: Friday, August 2, 2024 11:44 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: [hcp-users] Re: Human Connectome - Development Data Release Inquiry
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Joern Alexander Quent
Hello everyone,
I don't know why my responses to my previous e-mails got lost
when I tried to respond to Matt Glasser's reply about the event
file. I already replied twice but I think those e-mail never
arrived. Hence, I send a completely new e-mail. Please check below
for original e-mail (see
https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/qxil5R1EKPs/m/4G0ZZ9fUAQAJ
how the e-mails don't seem to be in the correct thread).
The content of ../EVs/trial_16.txt (also see attached) is
443.2113 13.9924 1
I am still puzzled what could be wrong because the content of
trial_16.txt is not different than the other event files. Any
advice would be greatly appreciated.
Best wishes,
Alex
Previous e-mail:
Glasser, Matthew
Perhaps send the file to the FSL group with the specific error about not having a valid triplet and they can debug this? This is an issue between your EV file and the FSL tool we are calling, so I don’t think
it is related to the HCP Pipelines.
Matt.
From: 'Joern Alexander Quent' via HCP-Users <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, August 5, 2024 at 3:13 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: [hcp-users] Help with TaskfMRILevel1.sh: ERROR running task fMRI using QuNex
Hello everyone,
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