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PennLINC / xcpEngine

Official public repository for the XCP Engine. This tool is deprecated in favor of XCP-D and ASLPrep.
MIT License
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Without error, but does not run fcon, qcfc, reho, alff and seed #377

Open nooshinjava opened 3 years ago

nooshinjava commented 3 years ago

Describe the bug I am using a default template (fc-36p_spkreg.dsn) and singularity run --cleanenv -B /XCP \ /XCP/simg/xcpEngine.simg \ -d /XCP/designs/fc-36p_spkreg.dsn \ -c /XCP/cohort_file/cohort_2.csv \ -o /XCP/xcpOutput \ -i /XCP/Work \ -t 1 it does not poduce directories related to fcon, qcfc, reho, alff and seed! Could you please help me, how to fix the problem? Thanks a lot in advance!

Cohort file Paste cohort file between the triple backticks

id0, id1,img
sub-B007Day1,FUNC,/XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_res-1_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=XCP/designs/fc-36p_spkreg.dsn
sequence=anatomical
standard=MNI%2x2x2

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

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc,seed

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

prestats_rerun[1]=0
prestats_cleanup[1]=0
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]=0
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_framewise[2]=fds:0.08,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

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

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

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

fcon_atlas[4]=schaefer
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_window[4]=10
fcon_pad[4]=FALSE
fcon_rerun[4]=1
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]=1
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]=1
alff_cleanup[6]=1

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

roiquant_atlas[7]=schaefer
roiquant_globals[7]=1
roiquant_vol[7]=1
roiquant_rerun[7]=1
roiquant_cleanup[7]=1

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

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

##################################################################
# 10 seed
###################################################################
seed_names[10]=AMC#
seed_radius[10]=8 # 8mm radius
seed_points[10]=-7,0,41#
seed_sptf[10]=gaussian
seed_smo[10]=6
seed_rerun[10]=1
seed_cleanup[10]=1

Error message Paste your error message between the backticks

Received options: -d /XCP/cohort_file/cohort_2.csv -o /XCP/xcpOutput -i XCP/Work -t 1
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][XCP/designs/fc-36p_spkreg.dsn]
· [I][XCP/Work]
· [C][XCP/cohort_file/cohort_2.csv]
· [O][XCP/xcpOutput]
· [M][Executing serially]
····································································
Date: 202008151235
UUID: 4562da78-8b5f-4a09-88a5-d10d53b7897e

Checking general dependencies
····································································
· Version AFNI           AFNI_19.3.17 
· 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-v1.0
· R version              3.3.3 
· R scripting front-end  3.3.3 
· · RNifti version       1.0.1
· · optparse version     1.6.4
· · 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                    ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

Current processing step:
@1 Localising subject metadata...
····································································
· @1.1 [Parsing subject identifiers]
· @1.1a [Creating output directory]
· @1.1b [XCP/xcpOutput/sub-B007Day1/FUNC]
· @1.2 [Initialising space mapping]
· @1.3 [Initialising derivative maps]
· @1.4 [Initialising atlas system]
· @1.5 Ingress
· @1.5.1 [Native space: sub-B007Day1_FUNC_fc_rest]
· @1.5.2a [Standard space: MNI]
· @1.5.3a [Anatomical space: sub-B007Day1_FUNC_anatomical]
source space map '' is not an image
· @1.5 [Priming analytic audit]
· @1.6 [Priming quality assessment]
····································································
Processing step complete:
Localising subject metadata...

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

Current processing step:
@3 Localising design
····································································
· @3.1 [Writing localised design]
· @3.2 [Evaluating subject variables]
····································································
Processing step complete:
Localising design

Localiser complete

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

[Delegating control to module]

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

[I][XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz]
[O][XCP/xcpOutput/sub-B007Day1/FUNC/prestats]
                             -   -   -
>> rln XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@0 Ensure matching orientation
····································································
· @0.1a Input: XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~.nii.gz
· @0.1b Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· @0.1c Output root:
· @0.1d checking the orientation of img and template
                             -   -   -
>> 3dinfo -orient XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~.nii.gz
                             -   -   -
>> 3dinfo -orient /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
NATIVE:LPI TEMPLATE:RPI
· @0.1e img and template orientation are not the same
· @0.1f make it: LPI -> RPI
                             -   -   -
>> 3dresample -orient RPI -inset XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~.nii.gz -prefix XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~_RPI.nii.gz
                             -   -   -
>> immv XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~_RPI.nii.gz XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~.nii.gz
· @0.1 

Current processing step:
@ getting data from fmriprep directory
····································································
                             -   -   -
>> immv XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~ XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~_FMP
                             -   -   -
>> cp XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_desc-confounds_regressors.tsv XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_fmriconf.tsv
cp: cannot stat 'XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_desc-confounds_regressors.tsv': No such file or directory
· @ checking refvolume and structural orientation
                             -   -   -
>> 3dresample -orient RPI -inset XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_res-1_boldref.nii.gz -prefix XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -overwrite
                             -   -   -
>> antsApplyTransforms -i XCP/fmriprep/sub-B007Day1/anat/sub-B007Day1_space-MNIPediatricAsym_cohort-6_desc-preproc_T1w.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_struct.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i XCP/fmriprep/sub-B007Day1/anat/sub-B007Day1_space-MNIPediatricAsym_cohort-6_dseg.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_segmentation.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
· @ generate mask and referenceVolumeBrain
                             -   -   -
>> antsApplyTransforms -i XCP/fmriprep/sub-B007Day1/anat/sub-B007Day1_space-MNIPediatricAsym_cohort-6_desc-brain_mask.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_structmask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_res-1_desc-brain_mask.nii.gz -mul XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_structmask.nii.gz XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz
                             -   -   -
>> antsApplyTransforms -i XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -mul XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolume.nii.gz XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -mul XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_struct.nii.gz XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_structbrain.nii.gz
· @ Quality assessment
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_segmentation.nii.gz -r XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_referenceVolumeBrain.nii.gz
· [Cross-correlation:    0.9372089 ]
· [Coverage:             0.9622516 ]
· [Jaccard coefficient:  0.9057486 ]
· [Dice coefficient:     0.9505436 ]
····································································
Processing step complete:
getting data from fmriprep directory
· @0.2 
                             -   -   -
>> imcp XCP/Work/sub-B007Day1_FUNC-prestats-583202486~TEMP~_FMP.nii.gz XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz
                             -   -   -
>> fslval XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_res-1_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz -t 2.000000
                             -   -   -
>> 3dresample -orient RPI -inset XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz -prefix XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz -overwrite
                             -   -   -
>> rln XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_preprocessed.nii.gz XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz
                             -   -   -
>> 10-9-1
                             -   -   -
>> 10-1

Module Workflow Map
····································································
· START
· @0
· @0.1a
· @0.1b
· @0.1c
· @0.1d
· @0.1e
· @0.1f
· @0.1
· @
· @
· @
· @
· @0.2
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz]
[O][XCP/xcpOutput/sub-B007Day1/FUNC/confound2]
                             -   -   -
>> rm -rf XCP/Work/sub-B007Day1_FUNC-confound2-361619367~TEMP~*
                             -   -   -
>> 0.08*2.000000
                             -   -   -
>> mkdir -p XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc

Current processing step:
@1 Generating confound matrix
····································································
· @1.1 Generating temporal mask
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j stdVARS -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_dvars-std.1D
Error in parse_args(OptionParser(option_list = option_list)) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Execution halted
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j rps -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_realignment.1D
Error in parse_args(OptionParser(option_list = option_list)) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Execution halted
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j fd -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D
Error in parse_args(OptionParser(option_list = option_list)) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Execution halted
· @1.1.1 [Computing framewise displacement]
                             -   -   -
>> ${XCPEDIR}/utils/fd.R -r XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_realignment.1D -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_fd.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_realignment.1D': No such file or directory
Execution halted
· @1.1.2 [Computing DVARS]
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_dvars -s XCP/Work/sub-B007Day1_FUNC-confound2-361619367~TEMP~
                             -   -   -
>> rm -f XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_spatial_sd.1D XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_ts_quality_index.1D XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_ts_outliers.1D
                             -   -   -
>> fslstats -t XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz -S
                             -   -   -
>> 3dTqual -automask XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz
                             -   -   -
>> 3dToutcount -automask XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_dvars-std.1D,XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D
· @1.1.3 [Selecting quality criteria]
                             -   -   -
>> rm -f XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC-nFlags.1D
· @1.1.4 [Quality criterion: fd < .16000000]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_fd.1D -t .16000000 -o XCP/Work/sub-B007Day1_FUNC-confound2-361619367~TEMP~_-fdMask.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_fd.1D': No such file or directory
Execution halted
/xcpEngine/core/functions/temporal_mask: line 146: XCP/Work/sub-B007Day1_FUNC-confound2-361619367~TEMP~_-fdMask.1D: No such file or directory
                             -   -   -
>> 0/0
Runtime error (func=(main), adr=10): Divide by zero
· @1.1.4 [Quality criterion: dvars < 2]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_dvars-std.1D -t 2 -o XCP/Work/sub-B007Day1_FUNC-confound2-361619367~TEMP~_-dvMask.1D
                             -   -   -
>> 17/200
· @1.1.5 [Applying framewise threshold to time series]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC-nFlags.1D -t 0.5 -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_tmask.1D -m 0
· @1.1.6 [Evaluating data quality]
· @1.2 relative maximum motion
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D -o max -f XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relMaxRMS.txt
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D': No such file or directory
Execution halted
· @1.3 relative mean motion
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D -o mean -f XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relMeanRMS.txt
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_relRMS.1D': No such file or directory
Execution halted
The nuisance matrix is being selected base on design files
· @1.2 Including realignment parameters
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x null -y XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_realignment.1D -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/mc/sub-B007Day1_FUNC_realignment.1D': No such file or directory
Execution halted
· @1.5 Including csf
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j csf -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_csf.1D
Error in parse_args(OptionParser(option_list = option_list)) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Execution halted
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D -y XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_csf.1D -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D': No such file or directory
Execution halted
· @1.8 Including wm
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j wm -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_wm.1D
Error in parse_args(OptionParser(option_list = option_list)) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Execution halted
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D -y XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_wm.1D -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D': No such file or directory
Execution halted
· @1.10 [Including 1 derivative(s)]
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D -y OPdx1 -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D': No such file or directory
Execution halted
· @1.11 [Including 2 power(s)]
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D -y OPpower2 -o XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D
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 'XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D': No such file or directory
Execution halted
                             -   -   -
>> fslnvols XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz
····································································
Processing step complete:
Generating confound matrix

Current processing step:
@2 Validating confound model
····································································
/xcpEngine/modules/confound2/confound2.mod: line 482: XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_confmat.1D: No such file or directory
                             -   -   -
>> rm -f XCP/xcpOutput/sub-B007Day1/FUNC/confound2/sub-B007Day1_FUNC_modelParameterCount.txt
· @2.1a 
····································································
Processing step complete:
Validating confound model

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.1.1
· @1.1.2
· @1.1.3
· @1.1.4
· @1.1.4
· @1.1.5
· @1.1.6
· @1.2
· @1.3
· @1.2
· @1.5
· @1.8
· @1.10
· @1.11
· @2
· @2.1a
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz]
[O][XCP/xcpOutput/sub-B007Day1/FUNC/regress]
                             -   -   -
>> rln XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz XCP/Work/sub-B007Day1_FUNC-regress-034911098~TEMP~.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
· @0.1 
Design files  
2.000000

Current processing step:
@7 Demeaning and detrending BOLD timeseries
····································································
· @7.2 
· @7.3 
· @7.5a [Applying polynomial detrend]
· @7.5b [Order: 2]
                             -   -   -
>> ${XCPEDIR}/utils/dmdt.R -d 2 -i XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz -o XCP/Work/sub-B007Day1_FUNC-regress-034911098~TEMP~_DMT.nii.gz -m XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -t ones
/xcpEngine/core/functions/exec_xcp: line 1: 29714 Killed                  ${XCPEDIR}/utils/"${@}"

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

Module Workflow Map
····································································
· START
· @0.1
· @7
· @7.2
· @7.3
· @7.5a
· @7.5b
· ERROR
····································································

····································································
· [An error occurred while processing module regress.]
· [The error was detected at signpost @7.5b.]
· [The most recent command logged was]
· [dmdt.R -d 2 -i XCP/xcpOutput/sub-B007Day1/FUNC/sub-B007Day1_FUNC.nii.gz -o XCP/Work/sub-B007Day1_FUNC-regress-034911098~TEMP~_DMT.nii.gz -m XCP/xcpOutput/sub-B007Day1/FUNC/prestats/sub-B007Day1_FUNC_mask.nii.gz -t ones]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: XCP/Work/sub-B007Day1_FUNC-regress-034911098~TEMP~_DMT.nii.gz]
· []
· [stream abort]
····································································

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

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

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

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ alff ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

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

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

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

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

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

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ seed ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-B007Day1_FUNC removed from analysis]
····································································
generating report

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

Runtime Information How were you running the software? Docker? Singularity? Directly? If Directly, please consider using Docker or Singluarity first before submitting a bug report.

Additional context Add any other context about the problem here.

a3sha2 commented 3 years ago

it look like your fmriprep output is not complete check if you have this file sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_desc-confounds_regressors.tsv in func directory

nooshinjava commented 3 years ago

Thanks, I have it with a different name: sub-B007Day2_task-rest_desc-confounds_regressors.tsv. Should I rename it?

nooshinjava commented 3 years ago

I have changed the name of the tsv file and still get the same error!

a3sha2 commented 3 years ago

there is problem with file name: you have sub-B007Day1* in cohort file and sub-B007Day2_task-rest_desc-confounds_regressors.tsv.if you have sub-B007Day1_task-rest_desc-confounds_regressors.tsv` it will work. check your fmriprep html if there is any error.

nooshinjava commented 3 years ago

it was just an example of the names. The output from fmriprep are completed without any error (I have double checked it just now :) ).

a3sha2 commented 3 years ago

when you change the name, change prestats_rerun[1]=0 to prestats_rerun[1]=1

nooshinjava commented 3 years ago

Trying all the possibilities, I still have the problem!

a3sha2 commented 3 years ago

@nooshinjava sorry fro late response. You can see from log file that xcp is looking for this file sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_desc-confounds_regressors.tsv and could not find it.

XCP/fmriprep/sub-B007Day1/func/sub-B007Day1_task-rest_space-MNIPediatricAsym_cohort-6_desc-confounds_regressors.tsv