Issue appeared with latest update

[Brainarea]

Describe the bug Re-preprocess data in a different folder with newest xcpengine docker image, resulted in multiple errors.

Cohort file Paste cohort file between the triple backticks

id0,img
sub-005,sub-005/ses-01/func/sub-005_ses-01_task-rest_space-MNI152NLin2009cAsym_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
#                  loc alised design files.
###################################################################

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

analysis=fc_$(whoami)
design=/designs/fc-36p_scrub.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]=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]=1
confound2_censor_contig[2]=1
confound2_framewise[2]=fds:0.04,rmss:0.05,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

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

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

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

fcon_atlas[4]=power264
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_window[4]=10
fcon_pad[4]=FALSE
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

Constructing a pipeline based on user specifications
····································································
· [D][/designs/fc-36p_scrub.dsn]
· [I][/scratch]
· [C][/cohort/cohort.csv]
· [O][/xcpOutput]
· [M][Executing serially]
····································································

Checking general dependencies
····································································
· Version AFNI           AFNI_19.1.18 
· 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       0.10.0
· · optparse version     1.6.2
· · pracma version       2.2.5
· · 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:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/xcpOutput/sub-005]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-005_anatomical]
· [Standard space: MNI]
· [Anatomical space: sub-005_anatomical]
source space map '' 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]
· [Evaluating subject variables]
····································································
Processing step complete:
Localising design

Localiser complete

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

[Delegating control to module]

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

[I][/xcpOutput/sub-005/sub-005.nii.gz]
[O][/xcpOutput/sub-005/prestats]

Current processing step:
Ensure matching orientation
····································································
· Input: /scratch/sub-005-prestats-954628706~TEMP~.nii.gz
· Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· Output root:
· checking the orientation of img and template
NATIVE:LPI TEMPLATE:RPI
· img and template orientation are not the same
· make it: LPI -> RPI

Current processing step:
getting data from fmriprep directory
····································································
· checking refvolume and structural orientation
· generate mask and referenceVolumeBrain
Image Exception : #22 :: ERROR: Could not open image sub-005_structmask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/xcpEngine/core/functions/exec_fsl: line 1:   805 Aborted                 ${FSLDIR}/bin/"${@}"
Cannot open volume /xcpOutput/sub-005/prestats/sub-005_mask for reading!
· generate new /xcpOutput/sub-005/sub-005_spaces.json with spaceMetadata
Cannot open volume /xcpOutput/sub-005/prestats/sub-005_mask for reading!
source space map '/xcpOutput/sub-005/prestats/sub-005_struct.nii.gz' is not an image
· Quality assessment
Error in readNifti(mask1path) : 
  Failed to read image from path /xcpOutput/sub-005/prestats/sub-005_segmentation.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(mask1path) :
  nifti_image_read: failed to find header file for '/xcpOutput/sub-005/prestats/sub-005_segmentation.nii.gz'
Execution halted
····································································
Processing step complete:
getting data from fmriprep directory

Module complete

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

[Delegating control to module]

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

[I][/xcpOutput/sub-005/sub-005.nii.gz]
[O][/xcpOutput/sub-005/confound2]

Current processing step:
Generating confound matrix
····································································
· Generating temporal mask
· [Computing framewise displacement]
· [Computing DVARS]
· [Selecting quality criteria]
· [Quality criterion: fd < .12000000]
· [Quality criterion: rel_rms < .15000000]
· [Quality criterion: dvars < 2]
· [Applying framewise threshold to time series]
· [Evaluating data quality]
· relative maximum motion
· relative mean motion
The nuisance matrix is being selected base on design files
· Including realignment parameters
· Including csf
· Including gsr
· Including wm
· [Including 1 derivative(s)]
· [Including 2 power(s)]
····································································
Processing step complete:
Generating confound matrix

Current processing step:
Validating confound model
····································································
····································································
Processing step complete:
Validating confound model

Module complete

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

[Delegating control to module]

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

[I][/xcpOutput/sub-005/sub-005.nii.gz]
[O][/xcpOutput/sub-005/regress]
Design files  
3.000000

Current processing step:
Demeaning and detrending BOLD timeseries
····································································
· [Applying polynomial detrend]
· [Order: 2]
· [Executing detrend: Confound matrix]
····································································
Processing step complete:
Demeaning and detrending BOLD timeseries

Current processing step:
Temporally filtering image and confounds
····································································
· [butterworth filter]
· [High pass frequency: 0.01]
· [Low pass frequency: 0.08]
· Interpolating over masked-out epochs...
· This will be slow
usage: interpolate.py [-h] -i IMG -o OUT -t TMASK [-m MASK] [-a REPTIME]
                      [-s OFREQ] [-f HIFREQ] [-v VOXBIN]
interpolate.py: error: argument -m/--mask: expected one argument
Error in dumpNifti(impath) : 
  Failed to read image from path /scratch/sub-005-regress-402719053~TEMP~_DMT_TMP_interpol.nii.gz
Calls: dumpNifti -> .Call
In addition: Warning message:
In dumpNifti(impath) :
  nifti_image_read: failed to find header file for '/scratch/sub-005-regress-402719053~TEMP~_DMT_TMP_interpol.nii.gz'
Execution halted

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

Module Workflow Map
····································································
· START
· @0.1
· @7
· @7.3
· @7.5a
· @7.5b
· @7.6
· @2
· @2.2
· @2.4.1
· @2.5
· @2.6
· @2.8
· @2.12a
· @2.12b
· @2.12c
· ERROR
····································································

····································································
· [An error occurred while processing module regress.]
· [The error was detected at signpost @2.12c.]
· [The most recent command logged was]
· [tfilter -i /scratch/sub-005-regress-402719053~TEMP~_DMT.nii.gz -o /scratch/sub-005-regress-402719053~TEMP~_DMT_TMP.nii.gz -a 3.000000 -f butterworth -h 0.01 -l 0.08 -n /xcpOutput/sub-005/confound2/mc/sub-005_tmask.1D -r 1 -d 2 -1 confmat:/scratch/sub-005-regress-402719053~TEMP~_DMT_confmat.1D]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /scratch/sub-005-regress-402719053~TEMP~_DMT_TMP.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-005 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-005 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-005 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-005 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-005 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-005 removed from analysis]
····································································
generating report

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

Runtime Information Docker

Additional context Add any other context about the problem here.

[a3sha2]

hi @orchid666 did you specify -r command? https://xcpengine.readthedocs.io/containers/index.html#using-xcpengine-with-singularity

[Brainarea]

yes i did, here is my docker command:

docker run --rm -it \
-v /Volumes/MISIU/Users/rnenert/Data/Epilepsy_CBD/fmriprep/preprocessed_nofs/xcpengine/cohort.csv:/cohort/cohort.csv \
-v /Volumes/MISIU/Users/rnenert/Data/Epilepsy_CBD/fmriprep/preprocessed_nofs/xcpengine/36_scrub:/xcpOutput \
-v /Volumes/MISIU/Users/rnenert/Data/Epilepsy_CBD/fmriprep/preprocessed_nofs/fmriprep:/relative \
-v /Volumes/MISIU/Users/rnenert/Data/Epilepsy_CBD/fmriprep/preprocessed_nofs/xcpengine/temp:/scratch \
-v /Volumes/Orchid/Rodolphe/Toolbox/xcpEngine_designs:/designs \
 pennbbl/xcpengine:latest \
-d /designs/fc-36p_scrub.dsn \
-c /cohort/cohort.csv \
-o /xcpOutput -m s \
-r /relative \
-i /scratch

[Brainarea]

Ok my bad i Identified the issue, my new run has a session number, which i forgot to include in the cohort file. Actually it still gives me the same error:

Current processing step:
getting data from fmriprep directory
····································································
· checking refvolume and structural orientation
· generate mask and referenceVolumeBrain
Image Exception : #22 :: ERROR: Could not open image sub-005_ses-01_structmask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/xcpEngine/core/functions/exec_fsl: line 1:   805 Aborted                 ${FSLDIR}/bin/"${@}"
Cannot open volume /xcpOutput/sub-005/ses-01/prestats/sub-005_ses-01_mask for reading!
· generate new /xcpOutput/sub-005/ses-01/sub-005_ses-01_spaces.json with spaceMetadata
Cannot open volume /xcpOutput/sub-005/ses-01/prestats/sub-005_ses-01_mask for reading!
source space map '/xcpOutput/sub-005/ses-01/prestats/sub-005_ses-01_struct.nii.gz' is not an image
· Quality assessment
Error in readNifti(mask1path) : 
  Failed to read image from path /xcpOutput/sub-005/ses-01/prestats/sub-005_ses-01_segmentation.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(mask1path) :
  nifti_image_read: failed to find header file for '/xcpOutput/sub-005/ses-01/prestats/sub-005_ses-01_segmentation.nii.gz'
Execution halted

[Brainarea]

Does xcpengine expect to have the session number in the anat files? Because anat files created by fmriprep do not have the session number.

[a3sha2]

No, session number is not compulsory

helps me check if you have the following in your fmriprep anat output

[Brainarea]

I appreciate the quick reply. Yes i do have those files, joining a screenshot: https://ibb.co/ryGR7qG

[a3sha2]

Thanks @orchid666 We just started testing the xcpEngine with multiple templates. You have more than 1 template in your output, MNI152Ln6 and MNI152Ln2009c can you remove MNI152Ln6 and try again. Multiple MNI templates is the problem.

[Brainarea]

Indeed , i removed the files and it seems to be working now. The MNI152Ln6 was automatically added because i used ICA-AROMA with fmriprep as specified in their doc: "ICA-AROMA denoising is performed in MNI152NLin6Asym space, which is automatically added to the list of --output-spaces if it was not already requested by the user. "

That could be a problem for people who want to use the Aroma denoising from xcpengine.

[a3sha2]

thank you! , we will update it

[Brainarea]

Hello, I actually encountered a new error, later in the processing. Is it possible that the MNI152Ln6 affected another thing?

Current processing step:
Converting BOLD timeseries to confound residuals
····································································
· [Computing confound correlations]
· [Executing detrend]

· [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
· @7.6
· @2
· @2.2
· @2.3
· @2.4.1
· @2.5
· @2.6
· @2.8
· @2.12a
· @2.12b
· @2.12c
· @3
· @3.1
· @3.2
· @4
· @4.2
· @4.3
· @4.5
· @4.6
· ERROR
····································································

····································································
· [An error occurred while processing module regress.]
· [The error was detected at signpost @4.6.]
· [The most recent command logged was]
· [3dTproject -input /scratch/sub-005_ses-01-regress-651608821~TEMP~_DMT_TMP.nii.gz -ort /xcpOutput/sub-005/ses-01/regress/sub-005_ses-01_confmat.1D -prefix /scratch/sub-005_ses-01-regress-651608821~TEMP~_DMT_TMP_REG.nii.gz]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /scratch/sub-005_ses-01-regress-651608821~TEMP~_DMT_TMP_REG.nii.gz]
· []
· [stream abort]
····································································

[a3sha2]

No, it is MNI152Ln6. More volumes is flagged . You need to check the threshold https://github.com/PennBBL/xcpEngine/blob/master/designs/fc-36p_scrub.dsn#L73 https://xcpengine.readthedocs.io/modules/regress.html#temporal-censoring