[RESOLVED] General_plot_bold_timeseries issue

Issues
1

Hello,
I have trouble running general_plot_bold_timeseries and I don’t know where is the log.

qunex_container general_plot_bold_timeseries \
    --images="/gpfs/gibbs/pi/n3/Studies/STIMZO/sessions/07010KB_J00/images/functional/bold1.nii.gz" \
    --elements="type=stats|imageindex=1|stats>statstype=fd,img=1>statstype=dvarsme,img=1;type=image|imageindex=1|name=V|img=1|mask=1;type=image|imageindex=1|name=WM|img=1|mask=1;type=image|imageindex=1|name=GM|img=1|mask=1" \
    --masks="$my_study_folder/sessions/07010KB_J00/images/segmentation/freesurfer/mri/aparc+aseg_bold.nii.gz" \
    --filename='07010KB_J00-BoldTSPlot.pdf' \
    --skip="0" \
    --sessions="07010KB_J00" \
    --verbose="true"
    --container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.94.14.sif" \
    --scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=40000,partition=day" \

When running it without container/scheduler parameters I only have a message saying: general_plot_bold_timeseries failed! Please check output / log!

Thanks!
Layla

2

Hi Layla,

Currently, this command only works with MATLAB but not Octave, which is why you were not able to run it with qunex_container. Can you try running the command without container and scheduler inside an interactive slurm job?

Lining