[RESOLVED] Issue running hcp4 / fMRIVolume

george.gifford · February 22, 2021, 9:58am

Hi,

I’m having an issue when running hcp4 / fMRIVolume. It reports having run successfully, but there is no output. Terminal output is below and the batch file is attached.

Thanks in advance for any help!

Best wishes,
George

Quantitative Neuroimaging Environment & Toolbox (Qu|Nex) Suite Version 0.61.17

=================================================================
gmri hcp4
–sessionids=“PSYC16023_Baseline”
–path=“/home/k1328096/qunex/PSYSCAN_test_qunex/”
–batchfile=“/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt”
–overwrite=“no”
–sessions=“/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt” \

Starting multiprocessing sessions in /home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt with a pool of 1 concurrent processes

---- Running local

Starting processing of sessions PSYC16023_Baseline at Thursday, 18. February 2021 19:19:40

Session id: PSYC16023_Baseline
[started on Thursday, 18. February 2021 19:19:40]
Running HCP fMRI Volume registration [HCPStyleData] …
—> PreFS results present.
—> FS results present.
—> PostFS results present.

Running 1 BOLD images in parallel

HCP fMRIVolume completed on Thursday, 18. February 2021 19:19:40

===> Final report for command hcp4
… PSYC16023_Baseline —> HCP fMRI Volume: bolds
===> Successful completion of all tasks

batch_psyscan_test.txt (2.0 KB)

aleksij.kraljic · February 22, 2021, 7:58pm

Hi George, we will assign a developer to this issue and will let you know once it has been resolved.

george.gifford · March 23, 2021, 2:45pm

Hi Aleksij,

Is there any news on this topic? Any help / advice would be hugely appreciated!

Best wishes,
George

alan.anticevic · March 25, 2021, 6:42pm

A post was split to a new topic: Spam Forum Posts

alan.anticevic · March 25, 2021, 6:47pm

@george.gifford Thank you for the follow up. The container tag you are using is now outdated because it was shared with you guys in the context of our HARMONY consortium. We will check if this issue is squashed and may be addressed in the upcoming public release candidate, which we should have out very soon. @zailyn will look into this as well.

alan.anticevic · March 25, 2021, 6:59pm

@george.gifford please can you review this issue reporting template:

What we need from you is:

Original call that you executed at the command line?
Can you please attach the full logs that should reside in:
/home/k1328096/qunex/PSYSCAN_test_qunex/processing/logs/comlogs/

There you should see files with one of the naming convention:

done_ fMRIVolume_ PSYC16023_Baseline_<time_stamp>.log → command completed
error_ fMRIVolume_ PSYC16023_Baseline_<time_stamp>.log → command errored out
tmp_ fMRIVolume_ PSYC16023_Baseline_<time_stamp>.log → it was interrupted

For details on the logging convention please see here:

For a detailed issue report please see here: [RESOLVED] Using runPALM on parcellated data gives 'Error using permute'

george.gifford · April 22, 2021, 2:01pm

Hi Alan,

Thanks for getting back to me. The full command and output at the terminal is below.

There is no output in /logs/comlogs/ but there is output in /runlogs/ which seems strange.

I’m attaching the batch file in case there is something I am doing wrong there!
batch_psyscan_test.txt (2.0 KB)

Many thanks,
George

[k1328096@login1 ~/qunex]0% ./qunexContainer hcp4
? --container=“${QUNEX_CONTAINER}”
? --sessions=“/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt”
? --sessionids=“PSYC16023_Baseline”
? --batchfile=“/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt”
? --overwrite=“no”
? --path=“/home/k1328096/qunex/PSYSCAN_test_qunex/”
[k1328096@login1 ~/qunex]0% → unsetting all environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis MSMBin HCPPIPEDIR_dMRITracFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW

Loading Quantitative Neuroimaging Environment & ToolboX (Qu|Nex) Version: v0.61.17

Logged in as User: k1328096
Node info: login1.nan.kcl.ac.uk
OS: RedHat Linux #1 SMP Tue Dec 15 08:51:23 CST 2020

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

                   DEVELOPED & MAINTAINED BY:  

                        Anticevic Lab                                     
                   MBLab led by Grega Repovs                              

                  COPYRIGHT & LICENSE NOTICE:

Use of this software is subject to the terms and conditions defined by the
Yale University Copyright Policies:
http://ocr.yale.edu/faculty/policies/yale-university-copyright-policy
and the terms and conditions defined in the file ‘LICENSE.md’ which is
a part of the Qu|Nex Suite source code package:
https://bitbucket.org/hidradev/qunextools/src/master/LICENSE.md

—> Setting up Octave

—> Qu|Nex environment set successfully!

… Running Qu|Nex v0.61.17 …

Using /home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt for input.

— Full Qu|Nex call for command: hcp4

gmri hcp4 --sessions=/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt --sessionids=PSYC16023_Baseline --batchfile=/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt --overwrite=no --path=/home/k1328096/qunex/PSYSCAN_test_qunex/

Quantitative Neuroimaging Environment & Toolbox (Qu|Nex) Suite Version 0.61.17

=================================================================
gmri hcp4
–sessionids=“PSYC16023_Baseline”
–path=“/home/k1328096/qunex/PSYSCAN_test_qunex/”
–batchfile=“/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt”
–overwrite=“no”
–sessions=“/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt” \

Starting multiprocessing sessions in /home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt with a pool of 1 concurrent processes

---- Running local

Starting processing of sessions PSYC16023_Baseline at Thursday, 18. February 2021 19:19:40

Session id: PSYC16023_Baseline
[started on Thursday, 18. February 2021 19:19:40]
Running HCP fMRI Volume registration [HCPStyleData] …
—> PreFS results present.
—> FS results present.
—> PostFS results present.

Running 1 BOLD images in parallel

HCP fMRIVolume completed on Thursday, 18. February 2021 19:19:40

===> Final report for command hcp4
… PSYC16023_Baseline —> HCP fMRI Volume: bolds
===> Successful completion of all tasks

alan.anticevic · May 4, 2021, 3:02pm

@george.gifford thank you for the detailed post. We captured this issue in our dev team and we will prioritize resolving this as soon as we get our release candidate deployed publicly, which is imminent now. I anticipate this issue may be solved in the latest release. Please check back on the forum for any upcoming release announcements.
A.

george.gifford · May 4, 2021, 3:09pm

Many thanks @alan.anticevic, I will wait for the public release.

Best wishes,
George

alan.anticevic · June 3, 2021, 6:16pm

@george.gifford the public release is now out officially. You can download it here:

https://qunex.yale.edu/qunex-registration/

Go ahead and register for the latest stable version and check if the issue above is now resolved. If not, please send us the logs and we will investigate.

george.gifford · June 9, 2021, 1:58pm

Hi @alan.anticevic,

Many thanks for the update, I will try the new version.

Best wishes,
George