Error when running the anatomical tutorial

[yangliu2009]

Describe the bug I built an XCP singularity container, and received the following error when running the anatomical tutorial rocessing failed to produce required output: /gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/xcp_output/sub-1/struc/sub-1_ExtractedBrain0N4.nii.gz]

Cohort file Paste cohort file between the triple backticks

id0,img
sub-1,fmriprep/sub-1/anat/sub-1_desc-preproc_T1w.nii.gz
...,...,...

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

#!/usr/bin/env bash

###################################################################
#  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  â  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete task-free functional connectivity pipeline.
# You may execute the analysis specified in this design file by
# calling (in any 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.
# * GLOBAL VARIABLES are used at all stages of all analyses.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the analysis
#                  stage during which they are used.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are sometimes 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=struc-ACCELERATOR
design=/gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/anat-antsct.dsn
sequence=anatomical
standard=MNI%1x1x1

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

pipeline=struc,gmd,jlf,roiquant,norm,qcanat

###################################################################
# 1 STRUC
###################################################################

struc_denoise_anat[1]=0
struc_prior_weight[1]=0.25
struc_posterior_formulation[1]='Socrates[1]'
struc_keepBEImages[1]=0
struc_floating_point[1]=0
struc_random_seed[1]=0
struc_bspline[1]=0
struc_fit[1]=0.3
struc_quick[1]=0
struc_seg_priors[1]=1
struc_rerun[1]=0
struc_cleanup[1]=1
struc_process[1]=ACT

###################################################################
# 2 GMD
###################################################################

gmd_rerun[2]=0
gmd_cleanup[2]=1

###################################################################
# 3 JLF
###################################################################

jlf_extract[3]=1 
jlf_keep_warps[3]=1
jlf_quick[3]=0
jlf_cohort[3]=Younger24
jlf_ncpu[3]=2
jlf_parallel[3]=1
jlf_rerun[3]=0
jlf_cleanup[3]=1

###################################################################
# 4 ROIQUANT
###################################################################

roiquant_atlas[4]=all
roiquant_vol[4]=1
roiquant_rerun[4]=0
roiquant_cleanup[4]=1

###################################################################
# 5 NORM
###################################################################

norm_primary[5]=1
norm_rerun[5]=0
norm_cleanup[5]=1

###################################################################
# 6 qcanat
###################################################################

qcanat_gm[6]=Y
qcanat_gm_val[6]=2,4
qcanat_wm[6]=Y
qcanat_wm_val[6]=3
qcanat_csf[6]=Y
qcanat_csf_val[6]=1
qcanat_cort[6]=Y
qcanat_cort_val[6]=4
qcanat_rerun[6]=0

Error message Paste your error message between the backticks

· [A major error has occurred.]
· [The processing stream will now abort.]
· [Preparing diagnostics]
····································································

Module Workflow Map
····································································
· START
· @0.1
· @0
· @0.1a
· @0.1b
· @0.1c
· @0.1d
· @1
· @1.1a
· @1.1b
· @1.1c
· @1.x
· ERROR
····································································

····································································
· [An error occurred while processing module struc.]
· [The error was detected at signpost @1.x.]
· [The most recent command logged was]
· [antsCorticalThickness.sh -d 3 -a /gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/xcp_output/sub-1/struc/sub-1~TEMP~.nii.gz -e /xcpEngine/space/MNI/MNI-1x1x1Head.nii.gz -m /xcpEngine/space/MNI/MNI-1x1x1BrainPrior.nii.gz -p /xcpEngine/space/MNI/MNI_priors/MNI-priors-%03d.nii.gz -o /gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/xcp_output/sub-1/struc/sub-1_ -s nii.gz -t /xcpEngine/space/MNI/MNI-1x1x1.nii.gz -f /xcpEngine/space/MNI/MNI-1x1x1MaskDilated.nii.gz -g 0 -w 0.25 -b Socrates[1] -j 0 -u 0 -v 0 -q 0]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/xcp_output/sub-1/struc/sub-1_ExtractedBrain0N4.nii.gz]
· []
· [stream abort]
····································································

Runtime Information export DATA_ROOT=/gpfs/home/yliu385/data/yliu385/Test/xcpengine/example/anatomical/ export sing=/gpfs/data/ccvstaff/user_services_test/xcpengine_new/xcpEngine.simg singularity run -B $DATA_ROOT $sing -d $DATA_ROOT/anat-antsct.dsn -c $DATA_ROOT/anat_cohort.csv -o $DATA_ROOT/xcp_output -t 1 -r $DATA_ROOT/

Additional context The singularity image was built from the docker image: singularity build xcpEngine.simg docker://pennbbl/xcpengine:latest