[RESOLVED] runPALM volume file generation failure: Error using subsasgn>assigndat

runPALM is failing to generate the volume file. Right and left surface files are generated successfully.


qunex runPALM \
    --image="/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/BOLD/BOLD.Dense.GBC.SCZ.dtseries.nii" \
    --design="name:/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within|d:dRB.Mean.SCZ|t:t1|eb:ebSCZ" \
    --args="n:100|accel:tail|twotail|zstat|demean" \
    --root="/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ" \


--> running PALM for CIFTI input
     ... started running PALM Volume at 2020-05-28 10:39:16, track progress in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_volume.log
     ... started running PALM Left Surface at 2020-05-28 10:39:16, track progress in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_left_surface.log
     ... started running PALM Right Surface at 2020-05-28 10:39:16, track progress in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_right_surface.log
     ... finished running PALM Volume (exit code: 1), log in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_volume.log
     ... finished running PALM Left Surface (exit code: 0), log in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_left_surface.log
     ... finished running PALM Right Surface (exit code: 0), log in /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_right_surface.log
     ... DONE
===> ERROR in completing runPALM:
     PALM failed
     The following PALM calls failed:
     - PALM Volume [/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_volume.log]
     Aborting further processing, please check files and logs!

Volume log file:


Relevant section of volume log:

Building null distribution.
1%	 [Design 1/1, Contrast 1/1, Shuffling 1/100, Modality 1/1]
	 Saving file: /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.RB.Mean.SCZ_volume_vox_ztstat
Error using subsasgn>assigndat (/opt/palm/palm-latest-o/fileio/@nifti/subsasgn.m:384)
Unknown filename extension (.SCZ_volume_vox_ztstat).
Error in subsasgn>fun (/opt/palm/palm-latest-o/fileio/@nifti/subsasgn.m:76->subsasgn>assigndat)
Error in subsasgn (/opt/palm/palm-latest-o/fileio/@nifti/subsasgn.m:20->subsasgn>fun)
Error in palm_miscwrite (/opt/palm/palm-latest-o/palm_miscwrite.m:94->subsasgn)
Error in palm_quicksave (/opt/palm/palm-latest-o/palm_quicksave.m:163->palm_miscwrite)
Error in palm_core (/opt/palm/palm-latest-o/palm_core.m:1609->palm_quicksave)
Error in palm (/opt/palm/palm-latest-o/palm.m:81->palm_core)

Left hemisphere log (completed successfully):


Container accessed via:

srun --pty -p pi_anticevic --time=2-00:00:00 --mem=20000 bash -l
singularity run /gpfs/project/fas/n3/software/Singularity/qunex_suite-latest.sif

@brendan.adkinson have you recently successfully ran other PALM analyses or does this error occur with each PALM call? The call to the PALM is the same as what we’ve successfully ran all the time in the past, so I wonder if the issue is with the latest PALM version. If this error is occuring for all the analyses with this version of the container, we’ll have to investigate if it is due to changes to PALM or octave.

Hi Grega - I have not used PALM recently. I think it’s been a while since others have used it via qunex as well, but I’m not positive. The only other PALM run I have tried also returned this error, however it was using this same data with a near-identical design, so I’m not sure how helpful that is in ruling out potential causes. Thanks for looking into this!

Ok. We’ll have to try the command on other data and track more in detail what the issue might be.

@brendan.adkinson this issue may be fully resolved now that the public release is out.

You can download it here:


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.