[RESOLVED] Using runPALM on parcellated data gives 'Error using permute'

Description:

runPALM appears unable to permute parcellated CIFTI files. The ptseries data seems to be read in Matlab as a file_array object, which cannot be permuted. This error does not appear when running dense CIFTI images. The error was first reported with PALM version alpha112 (versions alpha109 and prior did not have this issue).

Call:
Ran from:
/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within

Container tag qunex_suite-0.51.2.sif accessed via:

qunexContainer runPALM \
    --image="/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/BOLD/BOLD.Network.GBC.SCZ.ptseries.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|transposedata" \
    --root="/gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.Network.RB.Mean.SCZ" \
    --overwrite="yes" \
    --scheduler="SLURM,time=2-00:00:00,mem=20000,partition=pi_anticevic" \
    --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-latest.sif"

Logs:
None generated. Error in terminal output:

Running PALM alpha117 using Octave 4.4.1 with the following options:
-i /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.Network.RB.Mean.SCZ_i1_cifti.ptseries.nii
-d /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within_dRB.Mean.SCZ.csv
-t /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within_t1.csv
-eb /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within_ebSCZ.csv
-twotail
-zstat
-accel tail
-n 100
-transposedata
-demean
-o /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.Network.RB.Mean.SCZ
Found FSL in /opt/fsl/fsl-latest
Found FreeSurfer in /opt/freesurfer/freesurfer-6.0
Found HCP Workbench executable in /opt/workbench/workbench-latest/bin_rh_linux64/wb_command
Reading input 1/1: /gpfs/project/fas/n3/Studies/BlackThorn/analysis/PRT/2020/PALM/Within/PRT.Within.Network.RB.Mean.SCZ_i1_cifti.ptseries.nii
Error using permute (/opt/palm/palm-latest-o/fileio/@file_array/permute.m:10)
file_array objects can not be permuted.
Error in read_gifti_file>gifti_Data (/opt/palm/palm-latest-o/fileio/@gifti/private/read_gifti_file.m:201->permute)
Error in read_gifti_file>gifti_DataArray (/opt/palm/palm-latest-o/fileio/@gifti/private/read_gifti_file.m:122->read_gifti_file>gifti_Data)
Error in read_gifti_file (/opt/palm/palm-latest-o/fileio/@gifti/private/read_gifti_file.m:45->read_gifti_file>gifti_DataArray)
Error in gifti (/opt/palm/palm-latest-o/fileio/@gifti/gifti.m:89->read_gifti_file)
Error in palm_ciftiread (/opt/palm/palm-latest-o/palm_ciftiread.m:84->gifti)
Error in palm_miscread (/opt/palm/palm-latest-o/palm_miscread.m:161->palm_ciftiread)
Error in palm_ready (/opt/palm/palm-latest-o/palm_ready.m:47->palm_miscread)
Error in palm_takeargs (/opt/palm/palm-latest-o/palm_takeargs.m:1644->palm_ready)
Error in palm_core (/opt/palm/palm-latest-o/palm_core.m:33->palm_takeargs)
Error in palm (/opt/palm/palm-latest-o/palm.m:81->palm_core)

Hi Brendan, we’ve written to Anderson to ask about whether this might be a PALM issue. In the meantime, we will look into supporting an older version of PALM that works with parcellated CIFTI files.

@brendan.adkinson

Please use the latest public release is now out officially to check if this issue is resolved. 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.