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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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Fcon folder empty #267

Open tropical5th opened 4 years ago

tropical5th commented 4 years ago

Hi,

Thank you very much for making xcp pipeline available!

I have ran my data through it and for the most part it seems to have run successfully, however the fcon folder contains only empty files of zero bytes for all subjects.

I have attached the log file and my design file. The error folder is empty although I not that at the command line output states at one point:

/usr/local/lib/python3.5/dist-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
  warnings.warn(msg, category=DeprecationWarning)
Traceback (most recent call last):
  File "/usr/lib/python3.5/tkinter/__init__.py", line 36, in <module>
    import _tkinter
ImportError: No module named '_tkinter'

This surprises me a bit as I am running it from a singularity image

Any advice much appreciated,

Stephen

fc-36p_despike.txt

fc_k1517096_201911251414_LOG-process.txt

a3sha2 commented 4 years ago

is like you have run it several time before can you re run it with fresh directory

tropical5th commented 4 years ago

Ok thank you I'll try that

jasongong11 commented 4 years ago

Hi, I had a same issue even after refreshing the working and output dir. Could you please update if the issue has been solved or not? Thank you!

a3sha2 commented 4 years ago

can you post your error message @jasongong11

jasongong11 commented 4 years ago

Hi Azeez,

Sure! Please see the message:

generating report
/usr/local/lib/python3.5/dist-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
  warnings.warn(msg, category=DeprecationWarning)
Traceback (most recent call last):
  File "/usr/lib/python3.5/tkinter/__init__.py", line 36, in <module>
    import _tkinter
ImportError: No module named '_tkinter'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 9, in <module>
    from nilearn.plotting import (plot_epi, plot_matrix, plot_stat_map)
  File "/usr/local/lib/python3.5/dist-packages/nilearn/plotting/__init__.py", line 38, in <module>
    from .img_plotting import plot_img, plot_anat, plot_epi, \
  File "/usr/local/lib/python3.5/dist-packages/nilearn/plotting/img_plotting.py", line 28, in <module>
    import matplotlib.pyplot as plt
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/pyplot.py", line 2372, in <module>
    switch_backend(rcParams["backend"])
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/pyplot.py", line 207, in switch_backend
    backend_mod = importlib.import_module(backend_name)
  File "/usr/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/backends/backend_tkagg.py", line 1, in <module>
    from . import _backend_tk
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/backends/_backend_tk.py", line 5, in <module>
    import tkinter as Tk
  File "/usr/lib/python3.5/tkinter/__init__.py", line 38, in <module>
    raise ImportError(str(msg) + ', please install the python3-tk package')
ImportError: No module named '_tkinter', please install the python3-tk package
Sentry is attempting to send 0 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit

here is the code I used singularity run -B ~/Downloads:~/data /media/jasongong/Media/xcpEngine.simg -d ~/Downloads/fc-36p.dsn -c ~/Downloads/func_cohort.csv -o ~/data/xcp_output -t 1 -r ~/Downloads/fmriprep

Thanks!

jasongong11 commented 4 years ago

@a3sha2 Thank you for your help! Please see the above.

Best, Jason

a3sha2 commented 4 years ago

@jasongong11 sorry for late reply let see your log files pls

jasongong11 commented 4 years ago

@a3sha2 Yes! Sure! Thanks! Please see below, (sorry, it is a bit long...). I am not sure what is going wrong, but it looks everything works fine except the final output module.

Very much appreciated! 

$ singularity run -B /media/jasongong/Media/reading_r1/sub-01/derivatives:/home/user/data /media/jasongong/Media/xcpEngine.simg -d /home/user/data/fc-36p.dsn -c /home/user/data/cohort.csv -o /home/user/data/testoutput -r /home/user/data/fmriprep -t 1
Received options: -d /home/user/data/fc-36p.dsn -c /home/user/data/cohort.csv -o /home/user/data/testoutput -r /home/user/data/fmriprep -t 1
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][/home/user/data/fc-36p.dsn]
· [C][/home/user/data/cohort.csv]
· [O][/home/user/data/testoutput]
· [M][Executing serially]
····································································
Date: 202003252253
UUID: 2a1423d8-b0db-40f5-9fe6-121c5ae0f14e

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 [/home/user/data/testoutput/sub-01/task-rest]
· @1.2 [Initialising space mapping]
· @1.3 [Initialising derivative maps]
· @1.4 [Initialising atlas system]
· @1.5 Ingress
· @1.5.1 [Native space: sub-01_task-rest_anatomical]
· @1.5.2a [Standard space: MNI]
· @1.5.3a [Anatomical space: sub-01_task-rest_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][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/prestats]
                             -   -   -
>> rm -rf /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~*
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@0 Ensure matching orientation
····································································
· @0.1a Input: /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~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 /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~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 /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~.nii.gz -prefix /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~_RPI.nii.gz
                             -   -   -
>> immv /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~_RPI.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~.nii.gz
· @0.1 

Current processing step:
@ getting data from fmriprep directory
····································································
                             -   -   -
>> immv /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~ /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~_FMP
                             -   -   -
>> cp /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_desc-confounds_regressors.tsv /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv
· @ checking refvolume and structural orientation
                             -   -   -
>> 3dresample -orient RPI -inset /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_space-MNI152NLin2009cAsym_boldref.nii.gz -prefix /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -overwrite
                             -   -   -
>> antsApplyTransforms -i /home/user/data/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /home/user/data/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
· @ generate mask and referenceVolumeBrain
                             -   -   -
>> antsApplyTransforms -i /home/user/data/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_structmask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_structmask.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz
                             -   -   -
>> antsApplyTransforms -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_structbrain.nii.gz
· @ Quality assessment
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolumeBrain.nii.gz
· [Cross-correlation:    0.9726688 ]
· [Coverage:             0.9911698 ]
· [Jaccard coefficient:  0.9575488 ]
· [Dice coefficient:     0.9783141 ]
····································································
Processing step complete:
getting data from fmriprep directory
· @0.2 
                             -   -   -
>> imcp /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest~TEMP~_FMP.nii.gz /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz
                             -   -   -
>> fslval /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz -t 2.000000
                             -   -   -
>> 3dresample -orient RPI -inset /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz -prefix /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz -overwrite
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> 7-6-1
                             -   -   -
>> 7-1

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][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/confound2]
                             -   -   -
>> 0.167*2.000000
                             -   -   -
>> mkdir -p /home/user/data/testoutput/sub-01/task-rest/confound2/mc

Current processing step:
@1 Generating confound matrix
····································································
· @1.1 Generating temporal mask
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j stdVARS -o /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_dvars-std.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j rps -o /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_realignment.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j fd -o /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D
· @1.1.1 [Computing framewise displacement]
                             -   -   -
>> ${XCPEDIR}/utils/fd.R -r /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_realignment.1D -o /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_fd.1D
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_spatial_sd.1D /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_ts_quality_index.1D /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_ts_outliers.1D
                             -   -   -
>> fslstats -t /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz -S
                             -   -   -
>> 3dTqual -automask /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> 3dToutcount -automask /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_dvars-std.1D,/home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D
· @1.1.3 [Selecting quality criteria]
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest-nFlags.1D
· @1.1.4 [Quality criterion: fd < .334000000]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_fd.1D -t .334000000 -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest~TEMP~_-fdMask.1D
                             -   -   -
>> 1/150
· @1.1.4 [Quality criterion: dvars < 2]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_dvars-std.1D -t 2 -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest~TEMP~_-dvMask.1D
                             -   -   -
>> 2/150
· @1.1.5 [Applying framewise threshold to time series]
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest-nFlags.1D -t 0.5 -o /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_tmask.1D -m 0
· @1.1.6 [Evaluating data quality]
· @1.2 relative maximum motion
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D -o max -f /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relMaxRMS.txt
· @1.3 relative mean motion
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D -o mean -f /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relMeanRMS.txt
The nuisance matrix is being selected base on design files
· @1.2 Including realignment parameters
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x null -y /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_realignment.1D -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
· @1.5 Including csf
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j csf -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_csf.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -y /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_csf.1D -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
· @1.7 Including gsr
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j gsr -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_gsr.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -y /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_gsr.1D -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
· @1.8 Including wm
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_fmriconf.tsv -j wm -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_wm.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -y /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_wm.1D -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
· @1.10 [Including 1 derivative(s)]
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -y OPdx1 -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
· @1.11 [Including 2 power(s)]
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -y OPpower2 -o /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D
                             -   -   -
>> fslnvols /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
····································································
Processing step complete:
Generating confound matrix

Current processing step:
@2 Validating confound model
····································································
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_modelParameterCount.txt
· @2.1a 
····································································
Processing step complete:
Validating confound model

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.1.1
· @1.1.3
· @1.1.4
· @1.1.4
· @1.1.5
· @1.1.6
· @1.2
· @1.3
· @1.2
· @1.5
· @1.7
· @1.8
· @1.10
· @1.11
· @2
· @2.1a
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/regress]
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~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 
· @7.5a [Applying polynomial detrend]
· @7.5b [Order: 2]
                             -   -   -
>> ${XCPEDIR}/utils/dmdt.R -d 2 -i /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT.nii.gz -m /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz
· @7.6 [Executing detrend: Confound matrix]
                             -   -   -
>> ${XCPEDIR}/utils/1dDMDT.R -i /home/user/data/testoutput/sub-01/task-rest/confound2/sub-01_task-rest_confmat.1D -d 2 -o /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_confmat.1D
····································································
Processing step complete:
Demeaning and detrending BOLD timeseries

Current processing step:
@2 Temporally filtering image and confounds
····································································
· @2.2 
· @2.3 
· @2.5 
· @2.6 
· @2.8 
· @2.12a [butterworth filter]
· @2.12b [High pass frequency: 0.01]
· @2.12c [Low pass frequency: 0.08]
                             -   -   -
>> ${XCPEDIR}/utils/tfilter -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP.nii.gz -a 2.000000 -f butterworth -h 0.01 -l 0.08 -m /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r 1 -d 2 -1 confmat:/home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_confmat.1D
····································································
Processing step complete:
Temporally filtering image and confounds

Current processing step:
@4 Converting BOLD timeseries to confound residuals
····································································
· @4.2 
· @4.3 
                             -   -   -
>> mv /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP_confmat.1D /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_confmat.1D
· @4.5 [Computing confound correlations]
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_confmat.1D
· @4.6 [Executing detrend]
                             -   -   -
>> 3dTproject -input /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP.nii.gz -ort /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_confmat.1D -prefix /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP_REG.nii.gz
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -mul /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP_REG /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP_REG
····································································
Processing step complete:
Converting BOLD timeseries to confound residuals
· @0.2 
                             -   -   -
>> immv /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest~TEMP~_DMT_TMP_REG.nii.gz /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz
                             -   -   -
>> fslval /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -t 2.000000

Current processing step:
@6 Spatially filtering image
····································································
· @6.1 
· @6.2 [Configuring SUSAN]
· @6.4 
· @6.6 
· @6.10a [Filter: susan]
· @6.10b [Smoothing kernel: 6 mm]
· @6.11 
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_img_sm6.nii.gz -s susan -k 6 -m /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -u /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolumeBrain.nii.gz
····································································
Processing step complete:
Spatially filtering image
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> 7-6-1
                             -   -   -
>> 7-1

Module Workflow Map
····································································
· START
· @0.1
· @7
· @7.2
· @7.5a
· @7.5b
· @7.6
· @2
· @2.2
· @2.3
· @2.5
· @2.6
· @2.8
· @2.12a
· @2.12b
· @2.12c
· @4
· @4.2
· @4.3
· @4.5
· @4.6
· @0.2
· @6
· @6.1
· @6.2
· @6.4
· @6.6
· @6.10a
· @6.10b
· @6.11
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/fcon]
· @0.1 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/sub-01_task-rest_referenceVolume.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@1 Functional connectome: HarvardOxford
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz -R
                             -   -   -
>> 8058.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -l /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/HarvardOxford/sub-01_task-rest_HarvardOxford_network.txt
····································································
Processing step complete:
Functional connectome: HarvardOxford

Current processing step:
@1 Functional connectome: aal116
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/aal116/aal116MNI.nii.gz -R
                             -   -   -
>> 9170.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/aal116/aal116MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -l /xcpEngine/atlas/aal116/aal116NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/aal116/sub-01_task-rest_aal116_network.txt
····································································
Processing step complete:
Functional connectome: aal116

Current processing step:
@1 Functional connectome: desikanKilliany
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/desikanKilliany/desikanKillianyMNI.nii.gz -R
                             -   -   -
>> 2035.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/desikanKilliany/desikanKillianyMNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -l /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/desikanKilliany/sub-01_task-rest_desikanKilliany_network.txt
····································································
Processing step complete:
Functional connectome: desikanKilliany

Current processing step:
@1 Functional connectome: glasser360
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/glasser360/glasser360MNI.nii.gz -R
                             -   -   -
>> 360.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/glasser360/glasser360MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -l /xcpEngine/atlas/glasser360/glasser360NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/glasser360/sub-01_task-rest_glasser360_network.txt
····································································
Processing step complete:
Functional connectome: glasser360

Current processing step:
@1 Functional connectome: gordon333
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/gordon333/gordon333MNI.nii.gz -R
                             -   -   -
>> 333.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/gordon333/gordon333MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -l /xcpEngine/atlas/gordon333/gordon333NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/gordon333/sub-01_task-rest_gordon333_network.txt
····································································
Processing step complete:
Functional connectome: gordon333

Current processing step:
@1 Functional connectome: power264
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/power264/power264MNI.nii.gz -R
                             -   -   -
>> 264.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/power264/power264MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -l /xcpEngine/atlas/power264/power264NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/power264/sub-01_task-rest_power264_network.txt
····································································
Processing step complete:
Functional connectome: power264

Current processing step:
@1 Functional connectome: schaefer100x17
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer100x17/schaefer100x17MNI.nii.gz -R
                             -   -   -
>> 100.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer100x17/schaefer100x17MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -l /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x17/sub-01_task-rest_schaefer100x17_network.txt
····································································
Processing step complete:
Functional connectome: schaefer100x17

Current processing step:
@1 Functional connectome: schaefer100x7
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer100x7/schaefer100x7MNI.nii.gz -R
                             -   -   -
>> 100.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer100x7/schaefer100x7MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -l /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer100x7/sub-01_task-rest_schaefer100x7_network.txt
····································································
Processing step complete:
Functional connectome: schaefer100x7

Current processing step:
@1 Functional connectome: schaefer200x17
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer200x17/schaefer200x17MNI.nii.gz -R
                             -   -   -
>> 200.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer200x17/schaefer200x17MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -l /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x17/sub-01_task-rest_schaefer200x17_network.txt
····································································
Processing step complete:
Functional connectome: schaefer200x17

Current processing step:
@1 Functional connectome: schaefer200x7
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer200x7/schaefer200x7MNI.nii.gz -R
                             -   -   -
>> 200.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer200x7/schaefer200x7MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -l /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer200x7/sub-01_task-rest_schaefer200x7_network.txt
····································································
Processing step complete:
Functional connectome: schaefer200x7

Current processing step:
@1 Functional connectome: schaefer400x17
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -R
                             -   -   -
>> 400.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -l /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x17/sub-01_task-rest_schaefer400x17_network.txt
····································································
Processing step complete:
Functional connectome: schaefer400x17

Current processing step:
@1 Functional connectome: schaefer400x7
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer400x7/schaefer400x7MNI.nii.gz -R
                             -   -   -
>> 400.000000<=1
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer400x7/schaefer400x7MNI.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3 Computing network timeseries
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -l /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D
· @1.4 Computing adjacency matrix
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_network.txt
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7.net
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_missing.txt
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_network.txt -t N
· @1.5 Determining node coverage
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /home/user/data/testoutput/sub-01/task-rest/fcon/schaefer400x7/sub-01_task-rest_schaefer400x7_network.txt
····································································
Processing step complete:
Functional connectome: schaefer400x7

Module Workflow Map
····································································
· START
· @0.1
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· @1
· @1.2
· @1.2.2
· @1.3
· @1.4
· @1.5
· FINISH
····································································

Module complete

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

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                REGIONAL HOMOGENEITY MODULE                ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/reho]
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_referenceVolume.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@1 Computing voxelwise ReHo
····································································
· @1.1 Determining voxel neighbourhood
· @1.2c Vertices
· @1.3 Computing regional homogeneity (ReHo)
                             -   -   -
>> 3dReHo -prefix /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -inset /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz -nneigh 27
· @1.4 Standardising ReHo values
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -M
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -S
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -sub 0.366855 -div 0.127426 -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz
····································································
Processing step complete:
Computing voxelwise ReHo

Current processing step:
@2 Spatially filtering ReHo map
····································································
· @2.1a Filter: susan
· @2.2b Smoothing kernel: 6 mm
· @2.2 
· @2.4 
· @2.4.2 
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho_sm6.nii.gz -s susan -k 6 -m /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -u /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz
· @2.5 Standardising ReHo values
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho_sm6.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -M
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho_sm6.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -S
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho_sm6.nii.gz -sub 0.349168 -div 0.084000 -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ_sm6.nii.gz
····································································
Processing step complete:
Spatially filtering ReHo map
· @0.1 

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.2c
· @1.3
· @1.4
· @2
· @2.1a
· @2.2b
· @2.2
· @2.4
· @2.4.2
· @2.5
· @0.1
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/alff]
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_referenceVolume.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@1 Spatially filtering image
····································································
· @1.1 
· @1.2 [Configuring SUSAN]
· @1.4 
· @1.6 
· @1.7a 
····································································
Processing step complete:
Spatially filtering image

Current processing step:
@2 Amplitude of low-frequency fluctuations
····································································
· @2.0 At smoothness 0 mm
· @2.1 Ensuring integer periods
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz
                             -   -   -
>> fslnvols /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> fslval /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz pixdim4
· @2.3 
                             -   -   -
>> ln -s /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz
· @2.4 Computing power spectrum
                             -   -   -
>> fslpspec /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS.nii.gz
· @2.5 Computing square root of amplitudes
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS.nii.gz -sqrt /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SQRT.nii.gz
· @2.6 Extracting power spectrum at the low frequency band
                             -   -   -
>> 0.01*150*2.000000
                             -   -   -
>> 0.08*150*2.000000
                             -   -   -
>> 3.00000000-1
                             -   -   -
>> 24.00000000-3.00000000+1
· @2.7a 0.01 Hz is approximately position 2
· @2.7b of the power spectrum. There are about 22 frequency
· @2.7d positions corresponding to the passband (0.08 - 0.01 Hz)
· @2.7e in the power spectrum.
                             -   -   -
>> fslroi /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SQRT.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SLOW.nii.gz 2 22
· @2.8 Computing the amplitude of low-frequency fluctuations (ALFF)
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SLOW.nii.gz -Tmean -mul 22 /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz
· @2.9 Standardising ALFF values
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -M
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -S
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -sub 16043.460983 -div 8630.033086 -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz
· @2.0 At smoothness 6 mm
· @2.1 Ensuring integer periods
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz
                             -   -   -
>> fslnvols /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_img_sm6.nii.gz
                             -   -   -
>> fslval /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_img_sm6.nii.gz pixdim4
· @2.3 
                             -   -   -
>> ln -s /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_img_sm6.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz
· @2.4 Computing power spectrum
                             -   -   -
>> fslpspec /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~EVEN.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS.nii.gz
· @2.5 Computing square root of amplitudes
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS.nii.gz -sqrt /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SQRT.nii.gz
· @2.6 Extracting power spectrum at the low frequency band
                             -   -   -
>> 0.01*150*2.000000
                             -   -   -
>> 0.08*150*2.000000
                             -   -   -
>> 3.00000000-1
                             -   -   -
>> 24.00000000-3.00000000+1
· @2.7a 0.01 Hz is approximately position 2
· @2.7b of the power spectrum. There are about 22 frequency
· @2.7d positions corresponding to the passband (0.08 - 0.01 Hz)
· @2.7e in the power spectrum.
                             -   -   -
>> fslroi /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SQRT.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SLOW.nii.gz 2 22
· @2.8 Computing the amplitude of low-frequency fluctuations (ALFF)
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest~TEMP~PS-SLOW.nii.gz -Tmean -mul 22 /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff_sm6.nii.gz
· @2.9 Standardising ALFF values
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff_sm6.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -M
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff_sm6.nii.gz -k /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -S
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff_sm6.nii.gz -sub 7757.875572 -div 4090.461365 -mul /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ_sm6.nii.gz
····································································
Processing step complete:
Amplitude of low-frequency fluctuations
· @0.1 

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.2
· @1.4
· @1.6
· @1.7a
· @2
· @2.0
· @2.1
· @2.3
· @2.4
· @2.5
· @2.6
· @2.7a
· @2.7b
· @2.7d
· @2.7e
· @2.8
· @2.9
· @2.0
· @2.1
· @2.3
· @2.4
· @2.5
· @2.6
· @2.7a
· @2.7b
· @2.7d
· @2.7e
· @2.8
· @2.9
· @0.1
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/roiquant]
· @0.1 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolume.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest_referenceVolume.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
                             -   -   -
>> fslstats /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz -R

Current processing step:
@1 Regional quantification: HarvardOxford
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -x /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D -n /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -n HarvardOxford -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over HarvardOxford
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -n HarvardOxford -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over HarvardOxford
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -n HarvardOxford -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over HarvardOxford
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_HarvardOxford.nii.gz -n HarvardOxford -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_HarvardOxford_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over HarvardOxford
                             -   -   -
>> atlas_set HarvardOxford RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_alff.csv
                             -   -   -
>> atlas_set HarvardOxford RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_alffZ.csv
                             -   -   -
>> atlas_set HarvardOxford RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_reho.csv
                             -   -   -
>> atlas_set HarvardOxford RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/HarvardOxford/sub-01_task-rest_HarvardOxford_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: HarvardOxford

Current processing step:
@1 Regional quantification: aal116
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -x /xcpEngine/atlas/aal116/aal116NodeIndex.1D -n /xcpEngine/atlas/aal116/aal116NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -n aal116 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over aal116
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -n aal116 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over aal116
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -n aal116 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over aal116
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_aal116.nii.gz -n aal116 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_aal116_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over aal116
                             -   -   -
>> atlas_set aal116 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_alff.csv
                             -   -   -
>> atlas_set aal116 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_alffZ.csv
                             -   -   -
>> atlas_set aal116 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_reho.csv
                             -   -   -
>> atlas_set aal116 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/aal116/sub-01_task-rest_aal116_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: aal116

Current processing step:
@1 Regional quantification: desikanKilliany
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -x /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeIndex.1D -n /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -n desikanKilliany -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over desikanKilliany
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -n desikanKilliany -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over desikanKilliany
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -n desikanKilliany -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over desikanKilliany
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_desikanKilliany.nii.gz -n desikanKilliany -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_desikanKilliany_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over desikanKilliany
                             -   -   -
>> atlas_set desikanKilliany RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_alff.csv
                             -   -   -
>> atlas_set desikanKilliany RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_alffZ.csv
                             -   -   -
>> atlas_set desikanKilliany RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_reho.csv
                             -   -   -
>> atlas_set desikanKilliany RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/desikanKilliany/sub-01_task-rest_desikanKilliany_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: desikanKilliany

Current processing step:
@1 Regional quantification: glasser360
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -x /xcpEngine/atlas/glasser360/glasser360NodeIndex.1D -n /xcpEngine/atlas/glasser360/glasser360NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -n glasser360 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over glasser360
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -n glasser360 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over glasser360
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -n glasser360 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over glasser360
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_glasser360.nii.gz -n glasser360 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_glasser360_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over glasser360
                             -   -   -
>> atlas_set glasser360 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_alff.csv
                             -   -   -
>> atlas_set glasser360 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_alffZ.csv
                             -   -   -
>> atlas_set glasser360 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_reho.csv
                             -   -   -
>> atlas_set glasser360 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/glasser360/sub-01_task-rest_glasser360_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: glasser360

Current processing step:
@1 Regional quantification: gordon333
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -x /xcpEngine/atlas/gordon333/gordon333NodeIndex.1D -n /xcpEngine/atlas/gordon333/gordon333NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -n gordon333 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over gordon333
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -n gordon333 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over gordon333
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -n gordon333 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over gordon333
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_gordon333.nii.gz -n gordon333 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_gordon333_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over gordon333
                             -   -   -
>> atlas_set gordon333 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_alff.csv
                             -   -   -
>> atlas_set gordon333 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_alffZ.csv
                             -   -   -
>> atlas_set gordon333 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_reho.csv
                             -   -   -
>> atlas_set gordon333 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/gordon333/sub-01_task-rest_gordon333_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: gordon333

Current processing step:
@1 Regional quantification: power264
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -x /xcpEngine/atlas/power264/power264NodeIndex.1D -n /xcpEngine/atlas/power264/power264NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -n power264 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over power264
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -n power264 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over power264
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -n power264 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over power264
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_power264.nii.gz -n power264 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_power264_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over power264
                             -   -   -
>> atlas_set power264 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_alff.csv
                             -   -   -
>> atlas_set power264 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_alffZ.csv
                             -   -   -
>> atlas_set power264 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_reho.csv
                             -   -   -
>> atlas_set power264 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/power264/sub-01_task-rest_power264_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: power264

Current processing step:
@1 Regional quantification: schaefer100x17
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -x /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeIndex.1D -n /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -n schaefer100x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer100x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -n schaefer100x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer100x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -n schaefer100x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer100x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x17.nii.gz -n schaefer100x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer100x17
                             -   -   -
>> atlas_set schaefer100x17 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_alff.csv
                             -   -   -
>> atlas_set schaefer100x17 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer100x17 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_reho.csv
                             -   -   -
>> atlas_set schaefer100x17 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x17/sub-01_task-rest_schaefer100x17_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer100x17

Current processing step:
@1 Regional quantification: schaefer100x7
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -x /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeIndex.1D -n /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -n schaefer100x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer100x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -n schaefer100x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer100x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -n schaefer100x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer100x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer100x7.nii.gz -n schaefer100x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer100x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer100x7
                             -   -   -
>> atlas_set schaefer100x7 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_alff.csv
                             -   -   -
>> atlas_set schaefer100x7 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer100x7 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_reho.csv
                             -   -   -
>> atlas_set schaefer100x7 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer100x7/sub-01_task-rest_schaefer100x7_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer100x7

Current processing step:
@1 Regional quantification: schaefer200x17
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -x /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeIndex.1D -n /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -n schaefer200x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer200x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -n schaefer200x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer200x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -n schaefer200x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer200x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x17.nii.gz -n schaefer200x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer200x17
                             -   -   -
>> atlas_set schaefer200x17 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_alff.csv
                             -   -   -
>> atlas_set schaefer200x17 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer200x17 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_reho.csv
                             -   -   -
>> atlas_set schaefer200x17 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x17/sub-01_task-rest_schaefer200x17_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer200x17

Current processing step:
@1 Regional quantification: schaefer200x7
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -x /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeIndex.1D -n /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -n schaefer200x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer200x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -n schaefer200x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer200x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -n schaefer200x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer200x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer200x7.nii.gz -n schaefer200x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer200x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer200x7
                             -   -   -
>> atlas_set schaefer200x7 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_alff.csv
                             -   -   -
>> atlas_set schaefer200x7 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer200x7 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_reho.csv
                             -   -   -
>> atlas_set schaefer200x7 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer200x7/sub-01_task-rest_schaefer200x7_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer200x7

Current processing step:
@1 Regional quantification: schaefer400x17
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -x /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D -n /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -n schaefer400x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer400x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -n schaefer400x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer400x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -n schaefer400x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer400x17
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x17.nii.gz -n schaefer400x17 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x17_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer400x17
                             -   -   -
>> atlas_set schaefer400x17 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_alff.csv
                             -   -   -
>> atlas_set schaefer400x17 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer400x17 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_reho.csv
                             -   -   -
>> atlas_set schaefer400x17 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x17/sub-01_task-rest_schaefer400x17_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer400x17

Current processing step:
@1 Regional quantification: schaefer400x7
····································································
· @1.2 Mapping network to image space
· @1.2.1 
· @1.2.7 
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -x /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D -n /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -n schaefer400x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over schaefer400x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -n schaefer400x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over schaefer400x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -n schaefer400x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over schaefer400x7
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_schaefer400x7.nii.gz -n schaefer400x7 -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_schaefer400x7_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over schaefer400x7
                             -   -   -
>> atlas_set schaefer400x7 RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_alff.csv
                             -   -   -
>> atlas_set schaefer400x7 RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_alffZ.csv
                             -   -   -
>> atlas_set schaefer400x7 RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_reho.csv
                             -   -   -
>> atlas_set schaefer400x7 RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/schaefer400x7/sub-01_task-rest_schaefer400x7_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: schaefer400x7

Current processing step:
@1 Regional quantification: global
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz -x /xcpEngine/atlas/global/globalNodeIndex.1D -n /xcpEngine/atlas/global/globalNodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz -n global -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over global
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz -n global -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over global
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz -n global -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over global
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_global.nii.gz -n global -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_global_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over global
                             -   -   -
>> atlas_set global RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_alff.csv
                             -   -   -
>> atlas_set global RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_alffZ.csv
                             -   -   -
>> atlas_set global RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_reho.csv
                             -   -   -
>> atlas_set global RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/global/sub-01_task-rest_global_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: global

Current processing step:
@1 Regional quantification: segmentation
····································································
· @1.2 Mapping network to image space
· @1.2.2 
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation.nii.gz
                             -   -   -
>> 9-6-1
                             -   -   -
>> 9-1
· @1.3.3 
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz -x /xcpEngine/atlas/segmentation3/segmentation3NodeIndex.1D -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
· @1.3.4 Computing atlas statistics
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_alff.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_mean_alff -d anatomical_alff -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz -n segmentation -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alff over segmentation
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_alffZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_mean_alffZ -d anatomical_alffZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz -n segmentation -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_names.1D -p sub-01,task-rest -w 0
· Mean anatomical alffZ over segmentation
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_reho.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_mean_reho -d anatomical_reho -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz -n segmentation -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_names.1D -p sub-01,task-rest -w 0
· Mean anatomical reho over segmentation
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -s mean -o /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_rehoZ.csv -t /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_mean_rehoZ -d anatomical_rehoZ -a /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest_atlas/sub-01_task-rest_segmentation.nii.gz -n segmentation -i /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_idx.1D -r /home/user/data/testoutput/sub-01/task-rest/roiquant/sub-01_task-rest~TEMP~_segmentation_names.1D -p sub-01,task-rest -w 0
· Mean anatomical rehoZ over segmentation
                             -   -   -
>> atlas_set segmentation RegionalMeanAlff /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_alff.csv
                             -   -   -
>> atlas_set segmentation RegionalMeanAlffZ /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_alffZ.csv
                             -   -   -
>> atlas_set segmentation RegionalMeanReho /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_reho.csv
                             -   -   -
>> atlas_set segmentation RegionalMeanRehoZ /home/user/data/testoutput/sub-01/task-rest/roiquant/segmentation/sub-01_task-rest_segmentation_mean_rehoZ.csv
· @1.3.5 
· @1.3.6 
· @1.3.7 
· @1.3.8 
····································································
Processing step complete:
Regional quantification: segmentation

Module Workflow Map
····································································
· START
· @0.1
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.1
· @1.2.7
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.2
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· @1
· @1.2
· @1.2.2
· @1.3.3
· @1.3.4
· @1.3.5
· @1.3.6
· @1.3.7
· @1.3.8
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/norm]
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest~TEMP~.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1

Current processing step:
@1 Normalising using ANTs
····································································
· @1.1 [Selecting transforms to apply]
· @1.2 [Normalising primary dataset]
· @1.3 [Applying composite diffeomorphism to primary dataset]
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.4 [Applying composite diffeomorphism to derivative images:]
· @1.5 [alff]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_alffStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [alffZ]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_alffZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [alffZ_sm6]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alffZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_alffZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [alff_sm6]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/alff/sub-01_task-rest_alff_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_alff_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [img_sm6]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_img_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_img_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [mask]
· @1.6 
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_maskStd.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [referenceVolumeBrain]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_referenceVolumeBrain.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_referenceVolumeBrainStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [reho]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_rehoStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [rehoZ]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_rehoZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [rehoZ_sm6]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_rehoZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_rehoZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
· @1.5 [reho_sm6]
· @1.8 
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/reho/sub-01_task-rest_reho_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_reho_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
····································································
Processing step complete:
Normalising using ANTs
· @2.0 

Current processing step:
@2 Quality assessment
····································································
                             -   -   -
>> fslmaths /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_referenceVolumeBrainStd.nii.gz -bin /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest~TEMP~-seq2std_mask.nii.gz
· @2.1 [Computing registration quality metrics]
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest~TEMP~-seq2std_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· [Cross-correlation:    0.9295657 ]
· [Coverage:             0.9724757 ]
· [Jaccard coefficient:  0.9001203 ]
· [Dice coefficient:     0.9474351 ]
· @2.2 [Preparing slicewise rendering]
                             -   -   -
>> ${XCPEDIR}/utils/regslicer -s /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_referenceVolumeBrainStd.nii.gz -t /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -i /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest~TEMP~ -o /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_seq2std
····································································
Processing step complete:
Quality assessment
                             -   -   -
>> rln /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_std.nii.gz /home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz
                             -   -   -
>> 7-6-1
                             -   -   -
>> 7-1

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.2
· @1.3
· @1.4
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.6
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @1.5
· @1.8
· @2.0
· @2
· @2.1
· @2.2
· FINISH
····································································

Module complete

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

[Delegating control to module]

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

[I][/home/user/data/testoutput/sub-01/task-rest/sub-01_task-rest.nii.gz]
[O][/home/user/data/testoutput/sub-01/task-rest/qcfc]

Current processing step:
@1 Preparing depth map
····································································
· @1.1 Segmentation: /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz
· @1.2 Output: /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_depthMap.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/layerLabels -l /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_segmentation.nii.gz -i /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~ -o /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_depthMap.nii.gz
····································································
Processing step complete:
Preparing depth map

Current processing step:
@2 Aligning depth map
····································································
· @2.1 Resampling to 6mm isotropic: minimally preprocessed
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-pp-rs.nii.gz -inset /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_preprocessed.nii.gz -rmode Li
· @2.2 Resampling to 6mm isotropic: denoised
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-dn-rs.nii.gz -inset /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-dn.nii.gz -rmode Li
· @2.4 Aligning depth map to sequence space
                             -   -   -
>> 8-7-1
                             -   -   -
>> 8-1
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-onion-rs.nii.gz -inset /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-onion.nii.gz -rmode NN
····································································
Processing step complete:
Aligning depth map

Current processing step:
@3 Preparing summary graphics
····································································
· @3.1 Acquiring arguments
                             -   -   -
>> fslval /home/user/data/fmriprep/sub-01/func/sub-01_task-rest_acq-singleband_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> 0.167*2.000000 
                             -   -   -
>> 0.083*2.000000 
                             -   -   -
>> cp /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_dvars-std.1D /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_dvar.1D
                             -   -   -
>> cp /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_fd.1D /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_fd.1D
                             -   -   -
>> cp /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_rms1.1D
· @3.2 Generating visuals
                             -   -   -
>> ${XCPEDIR}/utils/voxts.R -i /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-pp-rs.nii.gz,/home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-dn-rs.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-onion-rs.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_voxts.png -t DV:/home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_dvar.1D:2,RMS:/home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_rms1.1D:.166000000,FD:/home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_fd.1D:.334000000 -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
····································································
Processing step complete:
Preparing summary graphics

Current processing step:
@4 Estimating loss of temporal degrees of freedom
····································································
                             -   -   -
>> rm -f /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_tdof.txt
· @4.1 36 nuisance parameters regressed
· @4.3 0 volumes censored
· @4.3 1 number of spikes FD
· @4.3 2 number of spikes FD
/xcpEngine/modules/qcfc/qcfc.mod: line 263: nSpikesDV: command not found
· @4.4 Total lost tDOF: 39
····································································
Processing step complete:
Estimating loss of temporal degrees of freedom

Current processing step:
@5 Estimating post-processing DVARS
····································································
· @5.1 [Computing DVARS]
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /home/user/data/testoutput/sub-01/task-rest/norm/sub-01_task-rest_referenceVolumeBrainStd.nii.gz -r /home/user/data/testoutput/sub-01/task-rest/prestats/sub-01_task-rest_struct.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-referenceVolumeBrain.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /home/user/data/testoutput/sub-01/task-rest/regress/sub-01_task-rest_residualised.nii.gz -o /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_dvars -s /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~ -d 1 -b /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~-referenceVolumeBrain.nii.gz
                             -   -   -
>> cp /home/user/data/testoutput/sub-01/task-rest/confound2/mc/sub-01_task-rest_relRMS.1D /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_rms.1D
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest_dvars-std.1D,/home/user/data/testoutput/sub-01/task-rest/qcfc/sub-01_task-rest~TEMP~_rms.1D
····································································
Processing step complete:
Estimating post-processing DVARS

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.2
· @2
· @2.1
· @2.2
· @2.4
· @3
· @3.1
· @3.2
· @4
· @4.1
· @4.3
· @4.3
· @4.3
· @4.4
· @5
· @5.1
· FINISH
····································································

Module complete
generating report
/usr/local/lib/python3.5/dist-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
  warnings.warn(msg, category=DeprecationWarning)
Traceback (most recent call last):
  File "/usr/lib/python3.5/tkinter/__init__.py", line 36, in <module>
    import _tkinter
ImportError: No module named '_tkinter'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 9, in <module>
    from nilearn.plotting import (plot_epi, plot_matrix, plot_stat_map)
  File "/usr/local/lib/python3.5/dist-packages/nilearn/plotting/__init__.py", line 38, in <module>
    from .img_plotting import plot_img, plot_anat, plot_epi, \
  File "/usr/local/lib/python3.5/dist-packages/nilearn/plotting/img_plotting.py", line 28, in <module>
    import matplotlib.pyplot as plt
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/pyplot.py", line 2372, in <module>
    switch_backend(rcParams["backend"])
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/pyplot.py", line 207, in switch_backend
    backend_mod = importlib.import_module(backend_name)
  File "/usr/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/backends/backend_tkagg.py", line 1, in <module>
    from . import _backend_tk
  File "/usr/local/lib/python3.5/dist-packages/matplotlib/backends/_backend_tk.py", line 5, in <module>
    import tkinter as Tk
  File "/usr/lib/python3.5/tkinter/__init__.py", line 38, in <module>
    raise ImportError(str(msg) + ', please install the python3-tk package')
ImportError: No module named '_tkinter', please install the python3-tk package
Sentry is attempting to send 0 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit

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jasongong11 commented 4 years ago

fc_jasongong_202003252253_sub-01_task-restLOG-process.txt

a3sha2 commented 4 years ago

the log file shows everything works well, fcon suppose have output pls can you pull for new docker or singularity image

jasongong11 commented 4 years ago

Sorry for the late response. The problem seems to be solved. Many thanks!