Error message:The primary analyte is not a valid image

Describe the bug I receive the below error message "The primary analyte is not a valid image" when using the pipeline with singularity. What is strange is that this only occurs for some of the scans and that when I rerun the scans that have failed they tend to then work without generating the error? I had a look at the other issues where the same error had been reported where it seems to suggest that this can be related to the singularity image but wasn't sure how to proceed further

set TEMP_COHORT='resting_state/preprocessing/temp/tempcohort_$SGE_TASK_ID.csv'

singularity run -B /data/project/petProject/PHNO_AMPH_Rob:${HOME}/data_bind\
  ${HOME}/singularity_images/xcpEngine_latest.simg\
  -c ${HOME}/data_bind/code/${TEMP_COHORT} \
  -d ${HOME}/data_bind/code/resting_state/preprocessing/fc-36p_despike.dsn \
  -r ${HOME}/data_bind/data/BIDS_data/ \
  -o ${HOME}/data_bind/results/func/resting_state/denoised/t1w_36pdespike/ \
  -t 2

Cohort file Paste cohort file between the triple backticks

id0,id1,img
sub-503,ses-A,/data/project/petProject/PHNO_AMPH_Rob/results/func/processed20/fmriprep/sub-503/ses-A/func/sub-503_ses-A_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz
sub-503,ses-B,/data/project/petProject/PHNO_AMPH_Rob/results/func/processed20/fmriprep/sub-503/ses-B/func/sub-503_ses-B_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz
sub-510,ses-A,/data/project/petProject/PHNO_AMPH_Rob/results/func/processed20/fmriprep/sub-510/ses-A/func/sub-510_ses-A_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz
sub-510,ses-B,/data/project/petProject/PHNO_AMPH_Rob/results/func/processed20/fmriprep/sub-510/ses-B/func/sub-510_ses-B_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz

Design File Paste your entire design (.dsn) file between the triple backticks

#!/usr/bin/env bash

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the module that
#                  calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are typically array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=fc_$(whoami)
design=/home/k1201869/data_bind/code/resting_state/preprocessing/fc-36p_despike.dsn
sequence=anatomical
standard=MNI%2x2x2

###################################################################
# PIPELINE
###################################################################

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,qcfc
#removed norm, previously prior to qcfc

###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP

###################################################################
# 2 CONFOUND2
###################################################################

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_framewise[2]=fds:0.167,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

###################################################################
# 3  REGRESS
###################################################################

regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_smo[3]=6
regress_sptf[3]=susan
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=1
regress_process[3]=DMT-DSP-TMP-REG

###################################################################
# 4 FCON
###################################################################

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_rerun[4]=0
fcon_cleanup[4]=1

###################################################################
# 5 REHO
###################################################################

reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=susan
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1

###################################################################
# 6 ALFF
###################################################################

alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=susan
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1

###################################################################
# 7 ROIQUANT
###################################################################

roiquant_atlas[7]=all
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=0
norm_cleanup[8]=1

##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message Paste your error message between the backticks


· [An error occurred while processing module localiser.]
· [The error was detected at signpost @2.1.]
· [The most recent command logged was]
· []
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [The primary analyte is not a valid image: /data/project/petProject/PHNO_AMPH_Rob/results/func/processed20/fmriprep/sub-523/ses-B/func/sub-523_ses-B_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz]
· []
· [stream abort]```

**Runtime Information**
Running with singularity.

PennLINC / xcpEngine

Error message:The primary analyte is not a valid image #427