Tao-ZJU commented 3 years ago

Describe the bug Hi experts, I could not run the xcpEngine correctly, there are several errors that I don't have any idea.Could you help me check it and give me any suggestions? Thinks!

Cohort file Paste cohort file between the triple backticks

id0,img
sub-NC001,sub-NC001/func/sub-NC001_task-rest_space-MNI152NLin2009cAsym_res-2_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=/data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn
sequence=fmri
standard=MNI%2x2x2

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

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,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_rerun[2]=0
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-TMP-REG

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

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
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 (this is the terminal output) Paste your error message between the backticks

xcpengine-docker -d /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn -c /data/1Neuroimaging_Studies/xcp_test2/cohort.csv -r /data/1Neuroimaging_Studies/xcp_test2/BIDS_data/derivatives/fmriprep/ -i /data/1Neuroimaging_Studies/xcp_test2/Temporary_Dir/ -o /data/1Neuroimaging_Studies/xcp_test2/xcp_Out/
['/home/xu/.local/bin/xcpengine-docker', '-d', '/data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn', '-c', '/data/1Neuroimaging_Studies/xcp_test2/cohort.csv', '-r', '/data/1Neuroimaging_Studies/xcp_test2/BIDS_data/derivatives/fmriprep/', '-i', '/data/1Neuroimaging_Studies/xcp_test2/Temporary_Dir/', '-o', '/data/1Neuroimaging_Studies/xcp_test2/xcp_Out/']
RUNNING: docker run --rm -it -v /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn:/design/design.dsn:ro -v /data/1Neuroimaging_Studies/xcp_test2/cohort.csv:/cohort/cohort.csv:ro -v /data/1Neuroimaging_Studies/xcp_test2/xcp_Out/:/xcpOutput -v /data/1Neuroimaging_Studies/xcp_test2/BIDS_data/derivatives/fmriprep/:/relative -v /data/1Neuroimaging_Studies/xcp_test2/Temporary_Dir/:/scratch pennbbl/xcpengine:latest -d /design/design.dsn -c /cohort/cohort.csv -o /xcpOutput -m s -r /relative -i /scratch
Received options: -d /design/design.dsn -c /cohort/cohort.csv -o /xcpOutput -m s -r /relative -i /scratch
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][/design/design.dsn]
INFO: /root/matlab/startup.m does not exist ... creating
sed: cannot rename /design/sedjfEz53: Device or resource busy
· [I][/scratch]
· [C][/cohort/cohort.csv]
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: write.table -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/cohort/cohort.csv': Read-only file system
Execution halted
· [O][/xcpOutput]
· [M][Executing serially]
····································································
Date: 202103101123
UUID: f7fe7723-58ce-4e62-9897-2ea5272cf92c

Checking general dependencies
····································································
· Version AFNI           AFNI_20.3.01 
· Version ANTs           3.0.0.0 
· Version FSL            fsl-5.0.10 
· Version C3D            1.1.0 
· Version JQ             jq-1.5
· Version XCP Engine     xcpEngine-v1.2.3
· R version              3.3.3 
· R scripting front-end  3.3.3 
· · RNifti version       1.2.3
· · optparse version     1.6.6
· · pracma version       2.2.9
· · signal version       0.7.6
····································································
All general dependencies are present.

Checking environment
All environmental variables are defined.

Checking module-specific dependencies

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                      XCP ★ ★ ★ ENGINE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ LOCALISER ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                   XCP ENGINE LOCALISER                    ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
/xcpEngine/core/parseArgsLocaliser: line 113: /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn: No such file or directory

Current processing step:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/xcpOutput/sub-NC001]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-NC001_native]
· [Anatomical space: sub-NC001_anatomical]
fixed '' is not an image
· [Priming analytic audit]
· [Priming quality assessment]
····································································
Processing step complete:
Localising subject metadata...

Current processing step:
Localising image
····································································
· [Verifying that images are present]
· [Conforming and localising images]
····································································
Processing step complete:
Localising image

Current processing step:
Localising design
····································································
· [Writing localised design]
/xcpEngine/core/functions/printx: line 2: /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn: No such file or directory
· [Evaluating subject variables]
cp: missing destination file operand after '/xcpOutput/sub-NC001/template.nii.gz'
Try 'cp --help' for more information.
····································································
Processing step complete:
Localising design

Localiser complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ prestats ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/prestats]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step:
Ensure matching orientation
····································································
· Input: /scratch/sub-NC001-prestats-912282729~TEMP~.nii.gz
· Template:
· Output root:
· checking the orientation of img and template
NATIVE:LPI TEMPLATE:
· img and template orientation are not the same
· make it: LPI -> 
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ confound2 ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
#                                                                 #
#  ·                   CONFOUND MODEL MODULE                   ·  #
#                                                                 #
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/confound2]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step:
Generating confound matrix
····································································
· Generating temporal mask
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [Computing framewise displacement]
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/xcpOutput/sub-NC001/confound2/mc/sub-NC001_realignment.1D': No such file or directory
Execution halted
· [Computing DVARS]
· [Selecting quality criteria]
· [Applying framewise threshold to time series]
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "m" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [Evaluating data quality]
/xcpEngine/core/functions/temporal_mask: line 197: /xcpOutput/sub-NC001/confound2/mc/sub-NC001_tmask.1D: No such file or directory
· relative maximum motion
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/xcpOutput/sub-NC001/confound2/mc/sub-NC001_relRMS.1D': No such file or directory
Execution halted
· relative mean motion
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/xcpOutput/sub-NC001/confound2/mc/sub-NC001_relRMS.1D': No such file or directory
Execution halted
The nuisance matrix is being selected base on design files
/xcpEngine/modules/confound2/confound2.mod: line 155: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 172: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 190: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 215: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 235: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 271: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")
/xcpEngine/modules/confound2/confound2.mod: line 300: ((: > 0 : syntax error: operand expected (error token is "> 0 ")
/xcpEngine/modules/confound2/confound2.mod: line 326: ((: > 1 : syntax error: operand expected (error token is "> 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 346: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 381: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/confound2/confound2.mod: line 403: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
····································································
Processing step complete:
Generating confound matrix

Current processing step:
Validating confound model
····································································
/xcpEngine/modules/confound2/confound2.mod: line 490: null: No such file or directory
····································································
Processing step complete:
Validating confound model
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ regress ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/regress]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
Design files  
2.000000
/xcpEngine/modules/regress/regress.mod: line 344: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")
/xcpEngine/modules/regress/regress.mod: line 370: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")

Current processing step:
Spatially filtering image
····································································
ls: cannot access '/relative/sub-NC001/func/sub-NC001_task-rest*bold.dtseries.nii': No such file or directory
ls: cannot access '/relative/sub-NC001/func/sub-NC001_task-rest*hemi-L*.func.gii': No such file or directory

ls: cannot access '/relative/sub-NC001/func/sub-NC001_task-rest*bold.dtseries.nii': No such file or directory
ls: cannot access '/relative/sub-NC001/func/sub-NC001_task-rest*_hemi-*.gii': No such file or directory
····································································
Processing step complete:
Spatially filtering image
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ fcon ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗               FUNCTIONAL CONNECTOME MODULE                ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/fcon]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

::XCP-WARNING: Functional connectome analysis has been requested,
  but no network maps have been provided.

  Skipping module

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ reho ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
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#                                                                 #
#  ⊗                REGIONAL HOMOGENEITY MODULE                ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
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[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/reho]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step:
Computing voxelwise ReHo
····································································
· Determining voxel neighbourhood
· Sphere of radius 2
· Computing regional homogeneity (ReHo)
· Standardising ReHo values
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC001/reho/sub-NC001_reho
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC001/reho/sub-NC001_reho
Cannot open volume /xcpOutput/sub-NC001/reho/sub-NC001_reho for reading!
····································································
Processing step complete:
Computing voxelwise ReHo
/xcpEngine/modules/reho/reho.mod: line 141: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ alff ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
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[Delegating control to module]

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#                                                                 #
#  ⊗      AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE       ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/alff]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step:
Spatially filtering image
····································································
····································································
Processing step complete:
Spatially filtering image

Current processing step:
Amplitude of low-frequency fluctuations
····································································
· At smoothness 0 mm
· Ensuring integer periods
· Odd volume count: Excising first volume
· Computing power spectrum
· Computing square root of amplitudes
· Extracting power spectrum at the low frequency band
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
· Hz is approximately position -1
· of the power spectrum. There are about 0 frequency
· positions corresponding to the passband ( -  Hz)
· in the power spectrum.
Image Exception : #21 :: Invalid ROI dimensions
· Computing the amplitude of low-frequency fluctuations (ALFF)
Cannot open volume /scratch/sub-NC001-alff-802652325~TEMP~PS-SLOW for reading!
· Standardising ALFF values
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC001/alff/sub-NC001_alff
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC001/alff/sub-NC001_alff
Cannot open volume /xcpOutput/sub-NC001/alff/sub-NC001_alff for reading!
····································································
Processing step complete:
Amplitude of low-frequency fluctuations
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ roiquant ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

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#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗             ATLAS-BASED QUANTIFICATION MODULE             ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/roiquant]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/modules/roiquant/roiquant.mod: line 100: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ norm ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

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#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                IMAGE NORMALISATION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/norm]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
cp: missing destination file operand after '/xcpOutput/sub-NC001/norm/template.nii.gz'
Try 'cp --help' for more information.

Current processing step:
Normalising using ANTs
····································································
· [Selecting transforms to apply]
· [Applying composite diffeomorphism to derivative images:]
····································································
Processing step complete:
Normalising using ANTs
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ qcfc ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

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#                                                                 #
#  ⊗           FUNCTIONAL QUALITY ASSESSMENT MODULE            ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/xcpOutput/sub-NC001/sub-NC001.nii.gz]
[O][/xcpOutput/sub-NC001/qcfc]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step:
Preparing depth map
····································································
· Segmentation:
· Output: /xcpOutput/sub-NC001/qcfc/sub-NC001_depthMap.nii.gz
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
readlink: invalid option -- 'i'
Try 'readlink --help' for more information.
___________________________________________________________________

Usage: layerLabels -l <labels> -o <output> <options>

Compulsory arguments:
 -l : Labels
      The raw label set.

 -o : Output path
      The path where the layered label set will be written.

Optional arguments:
 -i : Intermediate output path
      Path for input and output of temporary files (intermediates)
      (default: current directory)

····································································
Processing step complete:
Preparing depth map

Current processing step:
Aligning depth map
····································································
· Resampling to 6mm isotropic: minimally preprocessed
· Resampling to 6mm isotropic: denoised
· Aligning depth map to sequence space
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
····································································
Processing step complete:
Aligning depth map

Current processing step:
Preparing summary graphics
····································································
· Acquiring arguments
/xcpEngine/modules/qcfc/qcfc.mod: line 177: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
cp: missing destination file operand after '/scratch/sub-NC001-qcfc-862991233~TEMP~_fd.1D'
Try 'cp --help' for more information.
cp: missing destination file operand after '/scratch/sub-NC001-qcfc-862991233~TEMP~_rms1.1D'
Try 'cp --help' for more information.
· Generating visuals
Warning messages:
1: Use of `ts$value` is discouraged. Use `value` instead. 
2: Use of `ts$value` is discouraged. Use `value` instead. 
Error in readNifti(maskpath) : 
  Failed to read image from path /scratch/sub-NC001-qcfc-862991233~TEMP~-onion-rs.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(maskpath) :
  nifti_image_read: failed to find header file for '/scratch/sub-NC001-qcfc-862991233~TEMP~-onion-rs.nii.gz'
Execution halted
····································································
Processing step complete:
Preparing summary graphics

Current processing step:
Estimating loss of temporal degrees of freedom
····································································
· Not nuisance parameters regressed
· all volumes censored
/xcpEngine/modules/qcfc/qcfc.mod: line 263: nSpikesDV: command not found
· Total lost tDOF: 0
····································································
Processing step complete:
Estimating loss of temporal degrees of freedom

Current processing step:
Estimating post-processing DVARS
····································································
· [Computing DVARS]
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
___________________________________________________________________

Usage: dvars -i <input> -o <output> <options>

Compulsory arguments:
 -i : Input image
      The time series for which DVARS is to be computed

 -o : Output root
      The root path where all DVARS time series will be written.
      The following 1D files will be created:

      output_root-raw.1D : Raw DVARS time series
      output_root-std.1D : Globally standardised DVARS time series
      output-root-vox.1D : Voxelwise standardised DVARS time series

Optional arguments:
 -s : Scratch space/intermediate output path
      Path for input and output of temporary files (intermediates)
      (default: current directory)

 -m : Mean intensity image
      The mean voxelwise intensity of the input time series. This
      should have been derived before any demeaning steps.

 -b : Brain-extracted mean intensity image
      A brain extracted version of -m. There is no need to
      specify -m if -b is specified.

 -d : Demeaned input
      Indicates that the input data have been demeaned. If this
      flag is set, then either the -m or -b argument must also
      be passed with an appropriate pre-demeaning image.

/xcpEngine/modules/qcfc/qcfc.mod: line 292: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")
cp: missing destination file operand after '/scratch/sub-NC001-qcfc-862991233~TEMP~_rms.1D'
Try 'cp --help' for more information.
····································································
Processing step complete:
Estimating post-processing DVARS
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete
generating report
ls: cannot access '/xcpOutput/sub-NC001/regress/*svg': No such file or directory
Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 405, in <module>
    moving = load_img(outdir+'/norm/'+prefix+'_intensityStd.nii.gz')
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/image.py", line 1063, in load_img
    return check_niimg(img, wildcards=wildcards, dtype=dtype)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 251, in check_niimg
    raise ValueError("File not found: '%s'" % niimg)
ValueError: File not found: '/xcpOutput/sub-NC001/norm/sub-NC001_intensityStd.nii.gz'
Sentry is attempting to send 0 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit

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#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                     ANALYSIS COMPLETE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #

Runtime Information I run the software through xcpengine-docker

a3sha2 commented 3 years ago

can you try singularity image? Please what command did you ran? thank you Tao

Tao-ZJU commented 3 years ago

can you try singularity image? Please what command did you ran? thank you Tao

Sorry for the late reply. I could not get the singularity image, and use docker image to run xcpengine.

Command I ran : xcpengine-docker -d /media/xuxiaojun/data_ORICO/xcp_test2/fc-36p.dsn -c /media/xuxiaojun/data_ORICO/xcp_test2/cohort.csv -r /media/xuxiaojun/data_ORICO/xcp_test2/BIDS_data/derivatives/fmriprep/ -i /media/xuxiaojun/data_ORICO/xcp_test2/Temporary_Dir/ -o /media/xuxiaojun/data_ORICO/xcp_test2/xcp_Out/

Error Messages ['/home/xuxiaojun/.local/bin/xcpengine-docker', '-d', '/media/xuxiaojun/data_ORICO/xcp_test2/fc-36p.dsn', '-c', '/media/xuxiaojun/data_ORICO/xcp_test2/cohort.csv', '-r', '/media/xuxiaojun/data_ORICO/xcp_test2/BIDS_data/derivatives/fmriprep/', '-i', '/media/xuxiaojun/data_ORICO/xcp_test2/Temporary_Dir/', '-o', '/media/xuxiaojun/data_ORICO/xcp_test2/xcp_Out/'] RUNNING: docker run --rm -it -v /media/xuxiaojun/data_ORICO/xcp_test2/fc-36p.dsn:/design/design.dsn:ro -v /media/xuxiaojun/data_ORICO/xcp_test2/cohort.csv:/cohort/cohort.csv:ro -v /media/xuxiaojun/data_ORICO/xcp_test2/xcp_Out/:/xcpOutput -v /media/xuxiaojun/data_ORICO/xcp_test2/BIDS_data/derivatives/fmriprep/:/relative -v /media/xuxiaojun/data_ORICO/xcp_test2/Temporary_Dir/:/scratch pennbbl/xcpengine:latest -d /design/design.dsn -c /cohort/cohort.csv -o /xcpOutput -m s -r /relative -i /scratch Received options: -d /design/design.dsn -c /cohort/cohort.csv -o /xcpOutput -m s -r /relative -i /scratch $XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications ···································································· · [D][/design/design.dsn] INFO: /root/matlab/startup.m does not exist ... creating sed: cannot rename /design/sedRGa9Lm: Device or resource busy · [I][/scratch] · [C][/cohort/cohort.csv] Error in file(file, ifelse(append, "a", "w")) : cannot open the connection Calls: write.table -> file In addition: Warning message: In file(file, ifelse(append, "a", "w")) : cannot open file '/cohort/cohort.csv': Read-only file system Execution halted · [O][/xcpOutput] · [M][Executing serially] ···································································· Date: 202103302338 UUID: 3e815bea-1ca0-43bd-b1be-f698ebc2b4eb

Checking general dependencies ···································································· · Version AFNI AFNI_20.3.01 · Version ANTs 3.0.0.0 · Version FSL fsl-5.0.10 · Version C3D 1.1.0 · Version JQ jq-1.5 · Version XCP Engine xcpEngine-v1.2.3 · R version 3.3.3 · R scripting front-end 3.3.3 · · RNifti version 1.2.3 · · optparse version 1.6.6 · · pracma version 2.2.9 · · signal version 0.7.6 ···································································· All general dependencies are present.

Checking environment All environmental variables are defined.

Checking module-specific dependencies

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⊗ XCP ★ ★ ★ ENGINE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

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              CURRENTLY PROCESSING MODULE:
                     ★ LOCALISER ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

###################################################################

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

⊗ XCP ENGINE LOCALISER ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

################################################################### /xcpEngine/core/parseArgsLocaliser: line 113: /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn: No such file or directory

Current processing step: Localising subject metadata... ···································································· · [Parsing subject identifiers] · [Creating output directory] · [/xcpOutput/sub-NC026] · [Initialising space mapping] · [Initialising derivative maps] · [Initialising atlas system] · Ingress · [Native space: sub-NC026_native] · [Anatomical space: sub-NC026_anatomical] fixed '' is not an image · [Priming analytic audit] · [Priming quality assessment] ···································································· Processing step complete: Localising subject metadata...

Current processing step: Localising image ···································································· · [Verifying that images are present] · [Conforming and localising images] ···································································· Processing step complete: Localising image

Current processing step: Localising design ···································································· · [Writing localised design] /xcpEngine/core/functions/printx: line 2: /data/1Neuroimaging_Studies/xcp_test2/fc-36p.dsn: No such file or directory · [Evaluating subject variables] cp: missing destination file operand after '/xcpOutput/sub-NC026/template.nii.gz' Try 'cp --help' for more information. ···································································· Processing step complete: Localising design

Localiser complete

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              CURRENTLY PROCESSING MODULE:
                     ★ prestats ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

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[Delegating control to module]

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⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

⊗ FMRI PREPROCESSING MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/prestats] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step: Ensure matching orientation ···································································· · Input: /scratch/sub-NC026-prestats-384413039~TEMP~.nii.gz · Template: · Output root: · checking the orientation of img and template NATIVE:LPI TEMPLATE: · img and template orientation are not the same · make it: LPI -> /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ confound2 ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

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[Delegating control to module]

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· · · · · · · · · · · · · · · · · · · · ·

· CONFOUND MODEL MODULE ·

· · · · · · · · · · · · · · · · · · · · ·

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[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/confound2] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step: Generating confound matrix ···································································· · Generating temporal mask Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "i" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "i" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "i" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted · [Computing framewise displacement] Error in file(file, "rt") : cannot open the connection Calls: unname -> as.matrix -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/xcpOutput/sub-NC026/confound2/mc/sub-NC026_realignment.1D': No such file or directory Execution halted · [Computing DVARS] · [Selecting quality criteria] · [Applying framewise threshold to time series] Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "m" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted · [Evaluating data quality] /xcpEngine/core/functions/temporal_mask: line 197: /xcpOutput/sub-NC026/confound2/mc/sub-NC026_tmask.1D: No such file or directory · relative maximum motion Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/xcpOutput/sub-NC026/confound2/mc/sub-NC026_relRMS.1D': No such file or directory Execution halted · relative mean motion Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/xcpOutput/sub-NC026/confound2/mc/sub-NC026_relRMS.1D': No such file or directory Execution halted The nuisance matrix is being selected base on design files /xcpEngine/modules/confound2/confound2.mod: line 155: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 172: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 190: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 215: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 235: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 271: ((: != 0 : syntax error: operand expected (error token is "!= 0 ") /xcpEngine/modules/confound2/confound2.mod: line 300: ((: > 0 : syntax error: operand expected (error token is "> 0 ") /xcpEngine/modules/confound2/confound2.mod: line 326: ((: > 1 : syntax error: operand expected (error token is "> 1 ") /xcpEngine/modules/confound2/confound2.mod: line 346: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 381: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/confound2/confound2.mod: line 403: ((: == 1 : syntax error: operand expected (error token is "== 1 ") ···································································· Processing step complete: Generating confound matrix

Current processing step: Validating confound model ···································································· /xcpEngine/modules/confound2/confound2.mod: line 490: null: No such file or directory ···································································· Processing step complete: Validating confound model /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ regress ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

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⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

⊗ CONFOUND REGRESSION MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/regress] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ") Design files
2.000000 /xcpEngine/modules/regress/regress.mod: line 344: ((: != 0 : syntax error: operand expected (error token is "!= 0 ") /xcpEngine/modules/regress/regress.mod: line 370: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")

Current processing step: Spatially filtering image ···································································· ls: cannot access '/relative/sub-NC026/func/sub-NC026_task-restbold.dtseries.nii': No such file or directory ls: cannot access '/relative/sub-NC026/func/sub-NC026_task-resthemi-L*.func.gii': No such file or directory

ls: cannot access '/relative/sub-NC026/func/sub-NC026_task-restbold.dtseries.nii': No such file or directory ls: cannot access '/relative/sub-NC026/func/sub-NC026_task-rest_hemi-*.gii': No such file or directory ···································································· Processing step complete: Spatially filtering image /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ fcon ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

###################################################################

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⊗ FUNCTIONAL CONNECTOME MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/fcon] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

::XCP-WARNING: Functional connectome analysis has been requested, but no network maps have been provided.

Skipping module

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              CURRENTLY PROCESSING MODULE:
                     ★ reho ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

###################################################################

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

⊗ REGIONAL HOMOGENEITY MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/reho] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step: Computing voxelwise ReHo ···································································· · Determining voxel neighbourhood · Sphere of radius 2 · Computing regional homogeneity (ReHo) · Standardising ReHo values Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC026/reho/sub-NC026_reho Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC026/reho/sub-NC026_reho Cannot open volume /xcpOutput/sub-NC026/reho/sub-NC026_reho for reading! ···································································· Processing step complete: Computing voxelwise ReHo /xcpEngine/modules/reho/reho.mod: line 141: ((: != 0 : syntax error: operand expected (error token is "!= 0 ") /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ alff ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

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⊗ AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/alff] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step: Spatially filtering image ···································································· ···································································· Processing step complete: Spatially filtering image

Current processing step: Amplitude of low-frequency fluctuations ···································································· · At smoothness 0 mm · Ensuring integer periods · Odd volume count: Excising first volume · Computing power spectrum · Computing square root of amplitudes · Extracting power spectrum at the low frequency band (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error · Hz is approximately position -1 · of the power spectrum. There are about 0 frequency · positions corresponding to the passband ( - Hz) · in the power spectrum. Image Exception : #21 :: Invalid ROI dimensions · Computing the amplitude of low-frequency fluctuations (ALFF) Cannot open volume /scratch/sub-NC026-alff-403699574~TEMP~PS-SLOW for reading! · Standardising ALFF values Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC026/alff/sub-NC026_alff Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-NC026/alff/sub-NC026_alff Cannot open volume /xcpOutput/sub-NC026/alff/sub-NC026_alff for reading! ···································································· Processing step complete: Amplitude of low-frequency fluctuations /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ roiquant ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

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⊗ ATLAS-BASED QUANTIFICATION MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/roiquant] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/modules/roiquant/roiquant.mod: line 100: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ norm ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

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⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

⊗ IMAGE NORMALISATION MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/norm] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ") cp: missing destination file operand after '/xcpOutput/sub-NC026/norm/template.nii.gz' Try 'cp --help' for more information.

Current processing step: Normalising using ANTs ···································································· · [Selecting transforms to apply] · [Applying composite diffeomorphism to derivative images:] ···································································· Processing step complete: Normalising using ANTs /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ") /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete

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              CURRENTLY PROCESSING MODULE:
                     ★ qcfc ★

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

###################################################################

[Delegating control to module]

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⊗ FUNCTIONAL QUALITY ASSESSMENT MODULE ⊗

⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗

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[I][/xcpOutput/sub-NC026/sub-NC026.nii.gz] [O][/xcpOutput/sub-NC026/qcfc] /xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Current processing step: Preparing depth map ···································································· · Segmentation: · Output: /xcpOutput/sub-NC026/qcfc/sub-NC026_depthMap.nii.gz Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "i" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted readlink: invalid option -- 'i' Try 'readlink --help' for more information.

Usage: layerLabels -l -o

Compulsory arguments: -l : Labels The raw label set.

-o : Output path The path where the layered label set will be written.

Optional arguments: -i : Intermediate output path Path for input and output of temporary files (intermediates) (default: current directory)

···································································· Processing step complete: Preparing depth map

Current processing step: Aligning depth map ···································································· · Resampling to 6mm isotropic: minimally preprocessed · Resampling to 6mm isotropic: denoised · Aligning depth map to sequence space Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "n" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted ···································································· Processing step complete: Aligning depth map

Current processing step: Preparing summary graphics ···································································· · Acquiring arguments /xcpEngine/modules/qcfc/qcfc.mod: line 177: ((: == 1 : syntax error: operand expected (error token is "== 1 ") cp: missing destination file operand after '/scratch/sub-NC026-qcfc-138045199~TEMP~_fd.1D' Try 'cp --help' for more information. cp: missing destination file operand after '/scratch/sub-NC026-qcfc-138045199~TEMP~_rms1.1D' Try 'cp --help' for more information. · Generating visuals Warning messages: 1: Use of ts$value is discouraged. Use value instead. 2: Use of ts$value is discouraged. Use value instead. Error in readNifti(maskpath) : Failed to read image from path /scratch/sub-NC026-qcfc-138045199~TEMP~-onion-rs.nii.gz Calls: readNifti -> .Call In addition: Warning message: In readNifti(maskpath) : nifti_image_read: failed to find header file for '/scratch/sub-NC026-qcfc-138045199~TEMP~-onion-rs.nii.gz' Execution halted ···································································· Processing step complete: Preparing summary graphics

Current processing step: Estimating loss of temporal degrees of freedom ···································································· · Not nuisance parameters regressed · all volumes censored /xcpEngine/modules/qcfc/qcfc.mod: line 263: nSpikesDV: command not found · Total lost tDOF: 0 ···································································· Processing step complete: Estimating loss of temporal degrees of freedom

Current processing step: Estimating post-processing DVARS ···································································· · [Computing DVARS] Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : flag "n" requires an argument Calls: parse_args -> parse_options -> getopt_options Execution halted

Usage: dvars -i -o

Compulsory arguments: -i : Input image The time series for which DVARS is to be computed

-o : Output root The root path where all DVARS time series will be written. The following 1D files will be created:

  output_root-raw.1D : Raw DVARS time series
  output_root-std.1D : Globally standardised DVARS time series
  output-root-vox.1D : Voxelwise standardised DVARS time series

Optional arguments: -s : Scratch space/intermediate output path Path for input and output of temporary files (intermediates) (default: current directory)

-m : Mean intensity image The mean voxelwise intensity of the input time series. This should have been derived before any demeaning steps.

-b : Brain-extracted mean intensity image A brain extracted version of -m. There is no need to specify -m if -b is specified.

-d : Demeaned input Indicates that the input data have been demeaned. If this flag is set, then either the -m or -b argument must also be passed with an appropriate pre-demeaning image.

/xcpEngine/modules/qcfc/qcfc.mod: line 292: ((: != 0 : syntax error: operand expected (error token is "!= 0 ") cp: missing destination file operand after '/scratch/sub-NC026-qcfc-138045199~TEMP~_rms.1D' Try 'cp --help' for more information. ···································································· Processing step complete: Estimating post-processing DVARS /xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete generating report ls: cannot access '/xcpOutput/sub-NC026/regress/*svg': No such file or directory Traceback (most recent call last): File "/xcpEngine/core/report.py", line 405, in moving = load_img(outdir+'/norm/'+prefix+'_intensityStd.nii.gz') File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/image.py", line 1063, in load_img return check_niimg(img, wildcards=wildcards, dtype=dtype) File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 251, in check_niimg raise ValueError("File not found: '%s'" % niimg) ValueError: File not found: '/xcpOutput/sub-NC026/norm/sub-NC026_intensityStd.nii.gz' Sentry is attempting to send 0 pending error messages Waiting up to 2 seconds Press Ctrl-C to quit

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⊗ ANALYSIS COMPLETE ⊗

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Thank you!

Tao-ZJU commented 3 years ago

Sorry, I have not resolve this problem.

-----Original Messages----- From:"Benjamin Deck" @.> Sent Time:2021-05-06 23:23:36 (Thursday) To: PennLINC/xcpEngine @.> Cc: Tao-ZJU @.>, Mention @.> Subject: Re: [PennLINC/xcpEngine] xcpEngine get error (#433)

@a3sha2@Tao-ZJU I also had this issue.

Is there a resolution?

Docker call

docker run -it -m 150g --cpus='16' \ -v /Users/neurouser1/Documents/PRISM_pilot/xcp/:/data \ -v /Users/neurouser1/Documents/PRISM_pilot/scratch/:/tmp \ -v /Users/neurouser1/Documents/DP5/xcp/:/git_repo \ pennbbl/xcpengine:latest \ -c /data/cohorts/test/PRISM_restTest_cohort.csv \ -d /git_repo/xcp_git_repo/xcpEngine/designs/fc-36p_despike.dsn \ -o /data/xcpOut/ \ -i /tmp/ \ -r /data/docker run -it -m 150g --cpus='16' \ -v /Users/neurouser1/Documents/PRISM_pilot/xcp/:/data \ -v /Users/neurouser1/Documents/PRISM_pilot/scratch/:/tmp \ -v /Users/neurouser1/Documents/DP5/xcp/:/git_repo \ pennbbl/xcpengine:latest \ -c /data/cohorts/test/PRISM_restTest_cohort.csv \ -d /git_repo/xcp_git_repo/xcpEngine/designs/fc-36p_despike.dsn \ -o /data/xcpOut/ \ -i /tmp/ \ -r /data/

Design file is identical to the one on your github repo.

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BenSnowSipes commented 2 years ago

I am having this very same problem using the XCPEngine singularity on an HPC. An almost identical set of errors and no output files were generated. Could this be related to the problem in this thread? https://github.com/PennLINC/xcpEngine/issues/389#issuecomment-698903334

lollopasquini commented 2 years ago

did you ever solve this error?

benjaminsipes commented 2 years ago

My solution was to abandon the xcpengine-singularity command in favor of singularity run $XCPIMG, which works as intended.

PennLINC / xcpEngine

xcpEngine get error #433

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⊗ XCP ★ ★ ★ ENGINE ⊗

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⊗ XCP ENGINE LOCALISER ⊗

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⊗ FMRI PREPROCESSING MODULE ⊗

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· · · · · · · · · · · · · · · · · · · · ·

· CONFOUND MODEL MODULE ·

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⊗ CONFOUND REGRESSION MODULE ⊗

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⊗ FUNCTIONAL CONNECTOME MODULE ⊗

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⊗ REGIONAL HOMOGENEITY MODULE ⊗

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⊗ AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE ⊗

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⊗ ATLAS-BASED QUANTIFICATION MODULE ⊗

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⊗ IMAGE NORMALISATION MODULE ⊗

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⊗ FUNCTIONAL QUALITY ASSESSMENT MODULE ⊗

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⊗ ANALYSIS COMPLETE ⊗

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