Describe the bug
Hello,
I am trying to run xcpEngine to denoise the smoothed non-aggresive AROMA output from fmriperp (*space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz). The terminal runs for maybe a minute, generates a bunch of folders, and then crashes. Could you help me solve this issue? For more information see below.
Thanks
Lorenzo
Cohort file
Paste cohort file between the triple backticks
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/jux/BBL/projects/testACT/script/designfiles/fc-acompcor.dsn
sequence=anatomical
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]=0
confound2_rms[2]=0
confound2_wm[2]=0
confound2_csf[2]=0
confound2_gsr[2]=0
confound2_acompcor[2]=1
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=0
confound2_sq[2]=0
confound2_censor[2]=0
confound2_censor_contig[2]=0
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-TMP-REG
###################################################################
# 4 FCON
###################################################################
fcon_atlas[4]=power264
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]=power264
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
Last login: Thu Jun 2 14:41:34 on ttys002
Setting PATH=/Library/Frameworks/Python.framework/Versions/3.10/bin:/usr/local/fsl/bin:/Users/lorenzopasquini/.local/bin/fmriprep-docker:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/lorenzopasquini/.local/bin
lorenzopasquini@NEUR-065ML88-LT Ayahuasca_acute_Natal % xcpengine-docker -d /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/fc-acompcor_EDITED.dsn -c /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/cohort_test3.csv -r /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives/ -o /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives_acute_denoised/ -i /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/working_dir
['/Library/Frameworks/Python.framework/Versions/3.10/bin/xcpengine-docker', '-d', '/Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/fc-acompcor_EDITED.dsn', '-c', '/Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/cohort_test3.csv', '-r', '/Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives/', '-o', '/Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives_acute_denoised/', '-i', '/Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/working_dir']
RUNNING: docker run --rm -it -v /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/fc-acompcor_EDITED.dsn:/design/design.dsn:ro -v /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/cohort_test3.csv:/cohort/cohort.csv:ro -v /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives_acute_denoised/:/xcpOutput -v /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives/:/relative -v /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/working_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/sedAhC9tL: 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: 202206022151
UUID: cb54d0a7-a162-487f-8daa-5a6b42808161
Checking general dependencies
····································································
· Version AFNI AFNI_21.3.17
· Version ANTs 2.3.3.dev168-g29bdf
· Version FSL fsl-5.0.10
· Version C3D 1.0.0
· Version JQ jq-1.5
· Version XCP Engine xcpEngine-v1.2.4
· R version 3.6.3
· R scripting front-end 3.6.3
· · RNifti version 1.3.1
· · optparse version 1.7.1
· · pracma version 2.3.6
· · signal version 0.7.7
····································································
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/jux/BBL/projects/testACT/script/designfiles/fc-acompcor.dsn: No such file or directory
Current processing step:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/xcpOutput/sub-1]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-1_native]
· [Anatomical space: sub-1_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/jux/BBL/projects/testACT/script/designfiles/fc-acompcor.dsn: No such file or directory
· [Evaluating subject variables]
cp: missing destination file operand after '/xcpOutput/sub-1/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-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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-1-prestats-207070337~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-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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-1/confound2/mc/sub-1_realignment.1D': No such file or directory
Execution halted
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
· [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-1/confound2/mc/sub-1_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-1/confound2/mc/sub-1_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-1/confound2/mc/sub-1_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-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/regress]
/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 ")
Current processing step:
Spatially filtering image
····································································
····································································
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-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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]
###################################################################
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
# ⊗ REGIONAL HOMOGENEITY MODULE ⊗ #
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
###################################################################
[I][/xcpOutput/sub-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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-1/reho/sub-1_reho
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-1/reho/sub-1_reho
Cannot open volume /xcpOutput/sub-1/reho/sub-1_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
###################################################################
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
CURRENTLY PROCESSING MODULE:
★ alff ★
# #
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[Delegating control to module]
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# #
# ⊗ AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE ⊗ #
# #
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[I][/xcpOutput/sub-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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
· 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-1-alff-472013119~TEMP~PS-SLOW for reading!
· Standardising ALFF values
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-1/alff/sub-1_alff
Image Exception : #22 :: ERROR: Could not open image /xcpOutput/sub-1/alff/sub-1_alff
Cannot open volume /xcpOutput/sub-1/alff/sub-1_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 ★
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
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[Delegating control to module]
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# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
# ⊗ ATLAS-BASED QUANTIFICATION MODULE ⊗ #
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
###################################################################
[I][/xcpOutput/sub-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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 ★
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
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[Delegating control to module]
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# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
# ⊗ IMAGE NORMALISATION MODULE ⊗ #
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
###################################################################
[I][/xcpOutput/sub-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/norm]
/xcpEngine/core/functions/rerun: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
cp: missing destination file operand after '/xcpOutput/sub-1/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 ★
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
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[Delegating control to module]
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# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
# ⊗ FUNCTIONAL QUALITY ASSESSMENT MODULE ⊗ #
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
###################################################################
[I][/xcpOutput/sub-1/sub-1.nii.gz]
[O][/xcpOutput/sub-1/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-1/qcfc/sub-1_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-1-qcfc-889582505~TEMP~_fd.1D'
Try 'cp --help' for more information.
cp: missing destination file operand after '/scratch/sub-1-qcfc-889582505~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-1-qcfc-889582505~TEMP~-onion-rs.nii.gz
In addition: Warning message:
In readNifti(maskpath) :
nifti_image_read: failed to find header file for '/scratch/sub-1-qcfc-889582505~TEMP~-onion-rs.nii.gz'
Execution halted
····································································
Processing step complete:
Preparing summary graphics
Current processing step:
Estimating loss of temporal degrees of freedom
····································································
· 0 nuisance parameters regressed
· Not 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-1-qcfc-889582505~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
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/__init__.py:96: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
"Numpy arrays.", FutureWarning)
Traceback (most recent call last):
File "/xcpEngine/core/report.py", line 414, 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 1157, 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 271, in check_niimg
raise ValueError("File not found: '%s'" % niimg)
ValueError: File not found: '/xcpOutput/sub-1/norm/sub-1_intensityStd.nii.gz'
Sentry is attempting to send 2 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit
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# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
# #
# ⊗ ANALYSIS COMPLETE ⊗ #
# #
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
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Runtime Information
I am running xcpEngine on Docker. I use the following command:
xcpengine-docker -d /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/fc-acompcor_EDITED.dsn -c /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/cohort_test3.csv -r /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives/ -o /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives_acute_denoised/ -i /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/working_dir
Additional context
I updated user permission with chmod 777 for the design and csv file.
I saw there was a previous post regarding issues with MNI152NLin6Asym but I did not understand how to solve this problem.
Describe the bug Hello, I am trying to run xcpEngine to denoise the smoothed non-aggresive AROMA output from fmriperp (*space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz). The terminal runs for maybe a minute, generates a bunch of folders, and then crashes. Could you help me solve this issue? For more information see below. Thanks
Lorenzo
Cohort file Paste cohort file between the triple backticks
Design File Paste your entire design (
.dsn) file between the triple backticksError message Paste your error message between the backticks
Runtime Information I am running xcpEngine on Docker. I use the following command: xcpengine-docker -d /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/fc-acompcor_EDITED.dsn -c /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/cohort_test3.csv -r /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives/ -o /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/derivatives_acute_denoised/ -i /Users/lorenzopasquini/Desktop/Ayahuasca_acute_Natal/working_dir
Additional context I updated user permission with chmod 777 for the design and csv file. I saw there was a previous post regarding issues with MNI152NLin6Asym but I did not understand how to solve this problem.