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)