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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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xcpEngine combined with fmriprep 20.2.0rc1 #391

Open YukiSakai1209 opened 4 years ago

YukiSakai1209 commented 4 years ago

Describe the bug xcpEngine combined with fmriprep 20.2.0rc1. I cannot get normally preprocessed *resisualized.nii.gz. It must be related with the change of regressor names from confounds_regressors.tsv to confounds_timeseries.tsv ( https://github.com/poldracklab/fmriprep/commit/73e4ccde5080f2d66ba720bba03a13d270f8f65f ) in fmriprep 20.2.0rc1.

Cohort file

id0, id1,img
sub-01, ses-01, /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz

Design File Paste your entire design (.dsn) file between the triple backticks

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

analysis=fc_$(whoami)
design=/data/jux/BBL/projects/testACT/script/designfiles/fc-36p_despike.dsn
sequence=anatomical
standard=MNI%2x2x2

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

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

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

prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP

###################################################################
# 2 CONFOUND2
###################################################################

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_rerun[2]=1
confound2_cleanup[2]=1

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

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

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

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_rerun[4]=0
fcon_cleanup[4]=1

###################################################################
# 5 REHO
###################################################################

reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=susan
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1

###################################################################
# 6 ALFF
###################################################################

alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=susan
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1

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

roiquant_atlas[7]=all
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=0
norm_cleanup[8]=1

##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Runtime Information

Docker
a3sha2 commented 4 years ago

that is main issue, we are going to upgrade and let you know

a3sha2 commented 4 years ago

@YukiSakai1209
thank you, can you pull for new docker image (either latest or 1.2.3)

YukiSakai1209 commented 4 years ago

@a3sha2 Thank you very much for your very quick update. I pulled docker image again and tried. In general, xcpEngine seemed to read confound_timeseries.tsv file correctly. However, I encounterd the error below during the bandpass filtering step. Did you change those steps?

ｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷ
ｷ [An error occurred while processing module regress.]
ｷ [The error was detected at signpost @2.12c.]
ｷ [The most recent command logged was]
ｷ [tfilter -i /tmp/sub-01_ses-01-338872449~TEMP~_DMT_DSP.nii.gz -o /tmp/sub-01_ses-01-regress-338872449~TEMP~_DMT_DSP_TMP.nii.gz -a 3.000000 -f butterworth -h 0.01 -l 0.08 -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r 1 -d 2 -1]
ｷ [For additional details, view the processing log. For improved]
ｷ [diagnostics, increment verbosity using the -t option.]
ｷ []
ｷ [Processing failed to produce required output: /tmp/sub-01_ses-01-regress-338872449~TEMP~_DMT_DSP_TMP.nii.gz]
ｷ []
ｷ [stream abort]
ｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷｷ
a3sha2 commented 4 years ago

pls share with me the whole log file

YukiSakai1209 commented 4 years ago

Whole log file

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                   XCP ENGINE LOCALISER                    ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> 3dinfo -orient /tmp/sub-01_ses-01-prestats-560457880~TEMP~.nii.gz
                             -   -   -
>> 3dinfo -orient /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
                             -   -   -
>> immv /tmp/sub-01_ses-01-prestats-560457880~TEMP~ /tmp/sub-01_ses-01-prestats-560457880~TEMP~_FMP
                             -   -   -
>> 3dresample -orient LPI -inset /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz -prefix /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -overwrite
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_structmask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_structmask.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz
                             -   -   -
>> antsApplyTransforms -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_structbrain.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> imcp /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz
                             -   -   -
>> fslval /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -t 3.000000
                             -   -   -
>> 3dresample -orient LPI -inset /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -prefix /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -overwrite

###################################################################
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
#                                                                 #
#  ·                   CONFOUND MODEL MODULE                   ·  #
#                                                                 #
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
###################################################################
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j stdVARS -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j rps -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j fd -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/fd.R -r /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_fd.1D
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /out/sub-01/ses-01/sub-01_ses-01.nii.gz -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars -s /tmp/sub-01_ses-01-confound2-643240937~TEMP~
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tmean /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensity.nii.gz
                             -   -   -
>> bet /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensity.nii.gz /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensityBrain.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tperc 25 /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-lowerQuartile.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tperc 75 /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-upperQuartile.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-upperQuartile.nii.gz -sub /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-lowerQuartile.nii.gz -div 1.34897950039 /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-temporalSD.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -sub /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensity.nii.gz -Tar1 /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-temporalAR.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-temporalAR.nii.gz -mul -1 -add 1 -mul 2 -sqrt -mul /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-temporalSD.nii.gz /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-predictedSD.nii.gz
                             -   -   -
>> fslstats /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-predictedSD.nii.gz -k /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> fslnvols /out/sub-01/ses-01/sub-01_ses-01.nii.gz
                             -   -   -
>> fslroi /out/sub-01/ses-01/sub-01_ses-01.nii.gz /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t-1.nii.gz 0 199
                             -   -   -
>> fslroi /out/sub-01/ses-01/sub-01_ses-01.nii.gz /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t.nii.gz 1 200
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t-1.nii.gz -sqr /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-tdiff-sq.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-t-1.nii.gz -div /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-predictedSD.nii.gz -sqr /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-tdiff-vox-std.nii.gz
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-tdiff-sq.nii.gz -k /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-tdiff-vox-std.nii.gz -k /tmp/sub-01_ses-01-confound2-643240937~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D -o mean -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-mean.txt
                             -   -   -
>> fslstats -t /out/sub-01/ses-01/sub-01_ses-01.nii.gz -S
                             -   -   -
>> 3dTqual -automask /out/sub-01/ses-01/sub-01_ses-01.nii.gz
++ 3dTqual: AFNI version=AFNI_20.1.17 (Jun 20 2020) [64-bit]
++ Autoclip value = 9284.26
++ 79321 out of 381024 voxels survive the clip
++ Median=0.00733629  Median-3.5*MAD=0.00354792  Median+3.5*MAD=0.0111247
                             -   -   -
>> 3dToutcount -automask /out/sub-01/ses-01/sub-01_ses-01.nii.gz
++ 3dToutcount: AFNI version=AFNI_20.1.17 (Jun 20 2020) [64-bit]
++ 79752 voxels passed mask/clip
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D,/out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /out/sub-01/ses-01/sub-01_ses-01-nFlags.1D -t 0.5 -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_tmask.1D -m 0
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D -o max -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relMaxRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D -o mean -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relMeanRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x null -y /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j csf -o /out/sub-01/ses-01/confound2/sub-01_ses-01_csf.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_csf.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j gsr -o /out/sub-01/ses-01/confound2/sub-01_ses-01_gsr.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_gsr.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i -j wm -o /out/sub-01/ses-01/confound2/sub-01_ses-01_wm.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_wm.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y OPdx1 -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y OPpower2 -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> fslnvols /out/sub-01/ses-01/sub-01_ses-01.nii.gz

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> ${XCPEDIR}/utils/dmdt.R -d 2 -i /out/sub-01/ses-01/sub-01_ses-01.nii.gz -o /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT.nii.gz -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT
                             -   -   -
>> fslval /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT.nii.gz pixdim4
                             -   -   -
>> 3dDespike -prefix /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT_DSP.nii.gz -nomask -quiet -NEW /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT.nii.gz
++ 3dDespike: AFNI version=AFNI_20.1.17 (Jun 20 2020) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Elapsed despike time =  731ms
                             -   -   -
>> ${XCPEDIR}/utils/tfilter -i /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT_DSP.nii.gz -o /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT_DSP_TMP.nii.gz -a 3.000000 -f butterworth -h 0.01 -l 0.08 -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r 1 -d 2 -1
                             -   -   -
>> remove_ext /tmp/sub-01_ses-01-regress-015799748~TEMP~_DMT_DSP_TMP.nii.gz
a3sha2 commented 4 years ago

yes, thank you, I will get back to you soon

a3sha2 commented 4 years ago

@YukiSakai1209 thank you for your patience

try the latest singularity image and let me know if it works for you.

YukiSakai1209 commented 4 years ago

@a3sha2 Thank you very much. I have used docker version of xcpEngine, so far. Will it work as well?

a3sha2 commented 4 years ago

Yes, it will work

Get Outlook for iOShttps://aka.ms/o0ukef

From: YukiSakai1209 notifications@github.com Sent: Friday, September 25, 2020 8:43:54 PM To: PennBBL/xcpEngine xcpEngine@noreply.github.com Cc: Azeez Adebimpe azeez.adebimpe@outlook.com; Mention mention@noreply.github.com Subject: Re: [PennBBL/xcpEngine] xcpEngine combined with fmriprep 20.2.0rc1 (#391)

@a3sha2https://github.com/a3sha2 Thank you very much. I have used docker version of xcpEngine, so far. Will it work as well?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PennBBL/xcpEngine/issues/391#issuecomment-699247572, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACBXECUJZUEF7SVWGGSW4KLSHU2MVANCNFSM4RRQXVJQ.

YukiSakai1209 commented 4 years ago

@a3sha2 Thank you very much. I'll try it!

YukiSakai1209 commented 4 years ago

I tried the current 1.2.3 version. In general, everything works quite well in the volumetric space analysis. However, I cannot get the CIFTI output. I have the normal output of fmriprep including freesurfer/fsaverage and *task-rest_space-fsLR_den-91k_bold.dtseries.nii. How can I get the CIFTI output? The whole log was below.

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                   XCP ENGINE LOCALISER                    ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> 3dinfo -orient /tmp/sub-01_ses-01-prestats-933472794~TEMP~.nii.gz
                             -   -   -
>> 3dinfo -orient /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
                             -   -   -
>> immv /tmp/sub-01_ses-01-prestats-933472794~TEMP~ /tmp/sub-01_ses-01-prestats-933472794~TEMP~_FMP
                             -   -   -
>> 3dresample -orient LPI -inset /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz -prefix /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -overwrite
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /data/sub-01/ses-01/..//anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_structmask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_structmask.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz
                             -   -   -
>> antsApplyTransforms -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_structbrain.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> imcp /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz
                             -   -   -
>> fslval /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -o /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -t 3.000000
                             -   -   -
>> 3dresample -orient LPI -inset /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -prefix /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -overwrite

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

                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j stdVARS -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j rps -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j fd -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/fd.R -r /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_fd.1D
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /out/sub-01/ses-01/sub-01_ses-01.nii.gz -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars -s /tmp/sub-01_ses-01-confound2-500303948~TEMP~
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tmean /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensity.nii.gz
                             -   -   -
>> bet /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensity.nii.gz /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensityBrain.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tperc 25 /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-lowerQuartile.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -Tperc 75 /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-upperQuartile.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-upperQuartile.nii.gz -sub /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-lowerQuartile.nii.gz -div 1.34897950039 /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-temporalSD.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/sub-01_ses-01.nii.gz -sub /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensity.nii.gz -Tar1 /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-temporalAR.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-temporalAR.nii.gz -mul -1 -add 1 -mul 2 -sqrt -mul /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-temporalSD.nii.gz /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-predictedSD.nii.gz
                             -   -   -
>> fslstats /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-predictedSD.nii.gz -k /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> fslnvols /out/sub-01/ses-01/sub-01_ses-01.nii.gz
                             -   -   -
>> fslroi /out/sub-01/ses-01/sub-01_ses-01.nii.gz /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t-1.nii.gz 0 199
                             -   -   -
>> fslroi /out/sub-01/ses-01/sub-01_ses-01.nii.gz /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t.nii.gz 1 200
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t-1.nii.gz -sqr /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-tdiff-sq.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-t-1.nii.gz -div /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-predictedSD.nii.gz -sqr /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-tdiff-vox-std.nii.gz
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-tdiff-sq.nii.gz -k /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-tdiff-vox-std.nii.gz -k /tmp/sub-01_ses-01-confound2-500303948~TEMP~-dvars-meanIntensityBrain.nii.gz -M
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D -o mean -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-mean.txt
                             -   -   -
>> fslstats -t /out/sub-01/ses-01/sub-01_ses-01.nii.gz -S
                             -   -   -
>> 3dTqual -automask /out/sub-01/ses-01/sub-01_ses-01.nii.gz
++ 3dTqual: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
++ Autoclip value = 9282.59
++ 79462 out of 381024 voxels survive the clip
++ Median=0.00734788  Median-3.5*MAD=0.00351362  Median+3.5*MAD=0.0111821
                             -   -   -
>> 3dToutcount -automask /out/sub-01/ses-01/sub-01_ses-01.nii.gz
++ 3dToutcount: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
++ 79939 voxels passed mask/clip
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_dvars-std.1D,/out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /out/sub-01/ses-01/sub-01_ses-01-nFlags.1D -t 0.5 -o /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_tmask.1D -m 0
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D -o max -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relMaxRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relRMS.1D -o mean -f /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_relMeanRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x null -y /out/sub-01/ses-01/confound2/mc/sub-01_ses-01_realignment.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j csf -o /out/sub-01/ses-01/confound2/sub-01_ses-01_csf.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_csf.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j gsr -o /out/sub-01/ses-01/confound2/sub-01_ses-01_gsr.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_gsr.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_fmriconf.tsv -j wm -o /out/sub-01/ses-01/confound2/sub-01_ses-01_wm.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y /out/sub-01/ses-01/confound2/sub-01_ses-01_wm.1D -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y OPdx1 -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -y OPpower2 -o /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D
                             -   -   -
>> fslnvols /out/sub-01/ses-01/sub-01_ses-01.nii.gz

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> ${XCPEDIR}/utils/dmdt.R -d 2 -i /out/sub-01/ses-01/sub-01_ses-01.nii.gz -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT.nii.gz -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/1dDMDT.R -i /out/sub-01/ses-01/confound2/sub-01_ses-01_confmat.1D -d 2 -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_confmat.1D
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT
                             -   -   -
>> fslval /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT.nii.gz pixdim4
                             -   -   -
>> 3dDespike -prefix /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP.nii.gz -nomask -quiet -NEW /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT.nii.gz
++ 3dDespike: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Elapsed despike time =  722ms
                             -   -   -
>> ${XCPEDIR}/utils/1dDespike -i /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_confmat.1D -x /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_confmat.1D -r 1.000000 -n -q
                             -   -   -
>> 1dtranspose /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_confmat.1D /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike_tp.1D
                             -   -   -
>> fslascii2img /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike_tp.1D 36.00000000000000000000 1 1 200 1 1 1 1.000000 /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike.nii.gz
                             -   -   -
>> 3dcopy /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike.nii.gz /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike
++ 3dcopy: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file '/tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike.nii.gz'
                             -   -   -
>> 3dDespike -NEW -quiet -nomask -prefix /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike_despike /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike.1D
++ 3dDespike: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
++ Authored by: RW Cox
++ Elapsed despike time =  3ms
                             -   -   -
>> 1dtranspose /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_1dDespike-1dDespike_despike.1D /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/tfilter -i /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP.nii.gz -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP.nii.gz -a 3.000000 -f butterworth -h 0.01 -l 0.08 -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r 1 -d 2 -1 confmat:/tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_confmat.1D
                             -   -   -
>> remove_ext /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP.nii.gz
                             -   -   -
>> fslnvols /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP.nii.gz
                             -   -   -
>> fslval /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/genfilter.R -i /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP.nii.gz -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP.nii.gz -f butterworth -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -c 0.01 -l 0.08 -r 1 -d 2
                             -   -   -
>> ${XCPEDIR}/utils/1dGenfilter.R -i /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_confmat.1D -o /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_confmat.1D -f butterworth -t 1.000000 -c 0.01 -l 0.08 -r 1 -d 2
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/regress/sub-01_ses-01_confmat.1D
                             -   -   -
>> 3dTproject -input /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP.nii.gz -ort /out/sub-01/ses-01/regress/sub-01_ses-01_confmat.1D -prefix /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_REG.nii.gz
++ 3dTproject: AFNI version=AFNI_20.2.16 (Sep  2 2020) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Setting up regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
 + -- 36 other fixed ort regressors
++ 200 retained time points MINUS 39 regressors ==> 161 D.O.F. left
++ no -mask option ==> processing all 381024 voxels in dataset
++ Compute pseudo-inverse of fixed orts
++ Loading dataset
*+ WARNING: 3dTproject input data :: 302690 vectors are constant
++ Starting project-orization
++ Convert results to output dataset
++ Output dataset /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_REG.nii.gz
++ ===== clock time = 11s 337ms
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -mul /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_REG /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_REG
                             -   -   -
>> immv /tmp/sub-01_ses-01-regress-664101888~TEMP~_DMT_DSP_TMP_REG.nii.gz /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz
                             -   -   -
>> fslval /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -o /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -t 3.000000
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -o /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz -s susan -k 6 -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -u /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslstats /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -p 50
                             -   -   -
>> susan /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz 14866.68017550000000000000 2.54796540086508437971 3 1 1 /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz 14866.68017550000000000000 /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz
                             -   -   -
>> antsApplyTransforms -d 3 -e 3 -i -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -t /xcpEngine/utils/oneratiotransform.txt -o /out/sub-01/ses-01/regress/boldtoMNI.nii.gz -n LanczosWindowedSinc

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗               FUNCTIONAL CONNECTOME MODULE                ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> fslstats /xcpEngine/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -l /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/HarvardOxford/sub-01_ses-01_HarvardOxford_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/HarvardOxford/sub-01_ses-01_HarvardOxford_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/HarvardOxford/sub-01_ses-01_HarvardOxford_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/aal116/aal116MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/aal116/aal116MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -l /xcpEngine/atlas/aal116/aal116NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/aal116/sub-01_ses-01_aal116_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/aal116/sub-01_ses-01_aal116_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/aal116/sub-01_ses-01_aal116_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/desikanKilliany/desikanKillianyMNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/desikanKilliany/desikanKillianyMNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -l /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/desikanKilliany/sub-01_ses-01_desikanKilliany_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/desikanKilliany/sub-01_ses-01_desikanKilliany_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/desikanKilliany/sub-01_ses-01_desikanKilliany_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/glasser360/glasser360MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/glasser360/glasser360MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -l /xcpEngine/atlas/glasser360/glasser360NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/glasser360/sub-01_ses-01_glasser360_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/glasser360/sub-01_ses-01_glasser360_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/glasser360/sub-01_ses-01_glasser360_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/gordon333/gordon333MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/gordon333/gordon333MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -l /xcpEngine/atlas/gordon333/gordon333NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/gordon333/sub-01_ses-01_gordon333_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/gordon333/sub-01_ses-01_gordon333_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/gordon333/sub-01_ses-01_gordon333_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/power264/power264MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/power264/power264MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -l /xcpEngine/atlas/power264/power264NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/power264/sub-01_ses-01_power264_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/power264/sub-01_ses-01_power264_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/power264/sub-01_ses-01_power264_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer100x17/schaefer100x17MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer100x17/schaefer100x17MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -l /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer100x17/sub-01_ses-01_schaefer100x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer100x17/sub-01_ses-01_schaefer100x17_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer100x17/sub-01_ses-01_schaefer100x17_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer100x7/schaefer100x7MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer100x7/schaefer100x7MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -l /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer100x7/sub-01_ses-01_schaefer100x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer100x7/sub-01_ses-01_schaefer100x7_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer100x7/sub-01_ses-01_schaefer100x7_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer200x17/schaefer200x17MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer200x17/schaefer200x17MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -l /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer200x17/sub-01_ses-01_schaefer200x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer200x17/sub-01_ses-01_schaefer200x17_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer200x17/sub-01_ses-01_schaefer200x17_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer200x7/schaefer200x7MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer200x7/schaefer200x7MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -l /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer200x7/sub-01_ses-01_schaefer200x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer200x7/sub-01_ses-01_schaefer200x7_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer200x7/sub-01_ses-01_schaefer200x7_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -l /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer400x17/sub-01_ses-01_schaefer400x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer400x17/sub-01_ses-01_schaefer400x17_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer400x17/sub-01_ses-01_schaefer400x17_network.txt
                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer400x7/schaefer400x7MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer400x7/schaefer400x7MNI.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -l /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /out/sub-01/ses-01/fcon/schaefer400x7/sub-01_ses-01_schaefer400x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /out/sub-01/ses-01/fcon/schaefer400x7/sub-01_ses-01_schaefer400x7_network.txt -t N
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /out/sub-01/ses-01/fcon/schaefer400x7/sub-01_ses-01_schaefer400x7_network.txt

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                REGIONAL HOMOGENEITY MODULE                ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> 3dReHo -prefix /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -inset /out/sub-01/ses-01/sub-01_ses-01.nii.gz -nneigh 27
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Final vox neighbood: ellipsoid with Nneigh=27 and radii (1.900,1.900,1.900).
++ ReHo (Kendall's W) calculated.
                             -   -   -
>> fslstats /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -M
                             -   -   -
>> fslstats /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -sub 0.264305 -div 0.109754 -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -o /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -s susan -k 6 -m /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -u /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz
                             -   -   -
>> fslstats /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -p 50
                             -   -   -
>> susan /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz 14866.68017550000000000000 2.54796540086508437971 3 1 1 /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolume.nii.gz 14866.68017550000000000000 /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz
                             -   -   -
>> fslstats /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -M
                             -   -   -
>> fslstats /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -sub 0.251633 -div 0.082064 -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ_sm6.nii.gz

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗      AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE       ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> fslnvols /out/sub-01/ses-01/sub-01_ses-01.nii.gz
                             -   -   -
>> fslval /out/sub-01/ses-01/sub-01_ses-01.nii.gz pixdim4
                             -   -   -
>> fslpspec /tmp/sub-01_ses-01-alff-123590313~TEMP~EVEN.nii.gz /tmp/sub-01_ses-01-alff-123590313~TEMP~PS.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-alff-123590313~TEMP~PS.nii.gz -sqrt /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SQRT.nii.gz
                             -   -   -
>> fslroi /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SQRT.nii.gz /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SLOW.nii.gz 5 43
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SLOW.nii.gz -Tmean -mul 43 /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
                             -   -   -
>> fslstats /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -M
                             -   -   -
>> fslstats /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -sub 33851.352451 -div 17572.675129 -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
                             -   -   -
>> fslnvols /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz
                             -   -   -
>> fslval /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz pixdim4
                             -   -   -
>> fslpspec /tmp/sub-01_ses-01-alff-123590313~TEMP~EVEN.nii.gz /tmp/sub-01_ses-01-alff-123590313~TEMP~PS.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-alff-123590313~TEMP~PS.nii.gz -sqrt /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SQRT.nii.gz
                             -   -   -
>> fslroi /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SQRT.nii.gz /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SLOW.nii.gz 5 43
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-alff-123590313~TEMP~PS-SLOW.nii.gz -Tmean -mul 43 /out/sub-01/ses-01/alff/sub-01_ses-01_alff_sm6.nii.gz
                             -   -   -
>> fslstats /out/sub-01/ses-01/alff/sub-01_ses-01_alff_sm6.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -M
                             -   -   -
>> fslstats /out/sub-01/ses-01/alff/sub-01_ses-01_alff_sm6.nii.gz -k /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /out/sub-01/ses-01/alff/sub-01_ses-01_alff_sm6.nii.gz -sub 17803.956724 -div 8573.413251 -mul /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ_sm6.nii.gz

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗             ATLAS-BASED QUANTIFICATION MODULE             ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
                             -   -   -
>> fslstats /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -R
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -x /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D -n /xcpEngine/atlas/HarvardOxford/HarvardOxfordNodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -n HarvardOxford -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_alff-quantifyAtlas_HarvardOxford_mean.1D -a anatomical_alff_mean_HarvardOxford -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -n HarvardOxford -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_alffZ-quantifyAtlas_HarvardOxford_mean.1D -a anatomical_alffZ_mean_HarvardOxford -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -n HarvardOxford -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_reho-quantifyAtlas_HarvardOxford_mean.1D -a anatomical_reho_mean_HarvardOxford -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -n HarvardOxford -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_HarvardOxford.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_mean_rehoZ-quantifyAtlas_HarvardOxford_mean.1D -a anatomical_rehoZ_mean_HarvardOxford -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_HarvardOxford_names.1D -o /out/sub-01/ses-01/roiquant/HarvardOxford/sub-01_ses-01_HarvardOxford_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -x /xcpEngine/atlas/aal116/aal116NodeIndex.1D -n /xcpEngine/atlas/aal116/aal116NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -n aal116 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_alff-quantifyAtlas_aal116_mean.1D -a anatomical_alff_mean_aal116 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -n aal116 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_alffZ-quantifyAtlas_aal116_mean.1D -a anatomical_alffZ_mean_aal116 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -n aal116 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_reho-quantifyAtlas_aal116_mean.1D -a anatomical_reho_mean_aal116 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -n aal116 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_aal116.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_mean_rehoZ-quantifyAtlas_aal116_mean.1D -a anatomical_rehoZ_mean_aal116 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_aal116_names.1D -o /out/sub-01/ses-01/roiquant/aal116/sub-01_ses-01_aal116_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -x /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeIndex.1D -n /xcpEngine/atlas/desikanKilliany/desikanKillianyNodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -n desikanKilliany -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_alff-quantifyAtlas_desikanKilliany_mean.1D -a anatomical_alff_mean_desikanKilliany -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -n desikanKilliany -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_alffZ-quantifyAtlas_desikanKilliany_mean.1D -a anatomical_alffZ_mean_desikanKilliany -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -n desikanKilliany -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_reho-quantifyAtlas_desikanKilliany_mean.1D -a anatomical_reho_mean_desikanKilliany -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -n desikanKilliany -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_desikanKilliany.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_mean_rehoZ-quantifyAtlas_desikanKilliany_mean.1D -a anatomical_rehoZ_mean_desikanKilliany -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_desikanKilliany_names.1D -o /out/sub-01/ses-01/roiquant/desikanKilliany/sub-01_ses-01_desikanKilliany_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -x /xcpEngine/atlas/glasser360/glasser360NodeIndex.1D -n /xcpEngine/atlas/glasser360/glasser360NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -n glasser360 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_alff-quantifyAtlas_glasser360_mean.1D -a anatomical_alff_mean_glasser360 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -n glasser360 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_alffZ-quantifyAtlas_glasser360_mean.1D -a anatomical_alffZ_mean_glasser360 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -n glasser360 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_reho-quantifyAtlas_glasser360_mean.1D -a anatomical_reho_mean_glasser360 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -n glasser360 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_glasser360.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_mean_rehoZ-quantifyAtlas_glasser360_mean.1D -a anatomical_rehoZ_mean_glasser360 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_glasser360_names.1D -o /out/sub-01/ses-01/roiquant/glasser360/sub-01_ses-01_glasser360_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -x /xcpEngine/atlas/gordon333/gordon333NodeIndex.1D -n /xcpEngine/atlas/gordon333/gordon333NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -n gordon333 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_alff-quantifyAtlas_gordon333_mean.1D -a anatomical_alff_mean_gordon333 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -n gordon333 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_alffZ-quantifyAtlas_gordon333_mean.1D -a anatomical_alffZ_mean_gordon333 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -n gordon333 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_reho-quantifyAtlas_gordon333_mean.1D -a anatomical_reho_mean_gordon333 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -n gordon333 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_gordon333.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_mean_rehoZ-quantifyAtlas_gordon333_mean.1D -a anatomical_rehoZ_mean_gordon333 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_gordon333_names.1D -o /out/sub-01/ses-01/roiquant/gordon333/sub-01_ses-01_gordon333_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -x /xcpEngine/atlas/power264/power264NodeIndex.1D -n /xcpEngine/atlas/power264/power264NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -n power264 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_alff-quantifyAtlas_power264_mean.1D -a anatomical_alff_mean_power264 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -n power264 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_alffZ-quantifyAtlas_power264_mean.1D -a anatomical_alffZ_mean_power264 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -n power264 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_reho-quantifyAtlas_power264_mean.1D -a anatomical_reho_mean_power264 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -n power264 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_power264.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_mean_rehoZ-quantifyAtlas_power264_mean.1D -a anatomical_rehoZ_mean_power264 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_power264_names.1D -o /out/sub-01/ses-01/roiquant/power264/sub-01_ses-01_power264_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -x /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeIndex.1D -n /xcpEngine/atlas/schaefer100x17/schaefer100x17NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -n schaefer100x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_alff-quantifyAtlas_schaefer100x17_mean.1D -a anatomical_alff_mean_schaefer100x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -n schaefer100x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_alffZ-quantifyAtlas_schaefer100x17_mean.1D -a anatomical_alffZ_mean_schaefer100x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -n schaefer100x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_reho-quantifyAtlas_schaefer100x17_mean.1D -a anatomical_reho_mean_schaefer100x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -n schaefer100x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_mean_rehoZ-quantifyAtlas_schaefer100x17_mean.1D -a anatomical_rehoZ_mean_schaefer100x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x17/sub-01_ses-01_schaefer100x17_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -x /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeIndex.1D -n /xcpEngine/atlas/schaefer100x7/schaefer100x7NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -n schaefer100x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_alff-quantifyAtlas_schaefer100x7_mean.1D -a anatomical_alff_mean_schaefer100x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -n schaefer100x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_alffZ-quantifyAtlas_schaefer100x7_mean.1D -a anatomical_alffZ_mean_schaefer100x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -n schaefer100x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_reho-quantifyAtlas_schaefer100x7_mean.1D -a anatomical_reho_mean_schaefer100x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -n schaefer100x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer100x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_mean_rehoZ-quantifyAtlas_schaefer100x7_mean.1D -a anatomical_rehoZ_mean_schaefer100x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer100x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer100x7/sub-01_ses-01_schaefer100x7_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -x /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeIndex.1D -n /xcpEngine/atlas/schaefer200x17/schaefer200x17NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -n schaefer200x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_alff-quantifyAtlas_schaefer200x17_mean.1D -a anatomical_alff_mean_schaefer200x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -n schaefer200x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_alffZ-quantifyAtlas_schaefer200x17_mean.1D -a anatomical_alffZ_mean_schaefer200x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -n schaefer200x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_reho-quantifyAtlas_schaefer200x17_mean.1D -a anatomical_reho_mean_schaefer200x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -n schaefer200x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_mean_rehoZ-quantifyAtlas_schaefer200x17_mean.1D -a anatomical_rehoZ_mean_schaefer200x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x17/sub-01_ses-01_schaefer200x17_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -x /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeIndex.1D -n /xcpEngine/atlas/schaefer200x7/schaefer200x7NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -n schaefer200x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_alff-quantifyAtlas_schaefer200x7_mean.1D -a anatomical_alff_mean_schaefer200x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -n schaefer200x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_alffZ-quantifyAtlas_schaefer200x7_mean.1D -a anatomical_alffZ_mean_schaefer200x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -n schaefer200x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_reho-quantifyAtlas_schaefer200x7_mean.1D -a anatomical_reho_mean_schaefer200x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -n schaefer200x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer200x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_mean_rehoZ-quantifyAtlas_schaefer200x7_mean.1D -a anatomical_rehoZ_mean_schaefer200x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer200x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer200x7/sub-01_ses-01_schaefer200x7_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -x /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D -n /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -n schaefer400x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_alff-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_alff_mean_schaefer400x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -n schaefer400x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_alffZ-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_alffZ_mean_schaefer400x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -n schaefer400x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_reho-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_reho_mean_schaefer400x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -n schaefer400x17 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x17.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_mean_rehoZ-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_rehoZ_mean_schaefer400x17 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x17_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x17/sub-01_ses-01_schaefer400x17_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -x /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D -n /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -n schaefer400x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_alff-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_alff_mean_schaefer400x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -n schaefer400x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_alffZ-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_alffZ_mean_schaefer400x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -n schaefer400x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_reho-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_reho_mean_schaefer400x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -n schaefer400x7 -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_schaefer400x7.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_mean_rehoZ-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_rehoZ_mean_schaefer400x7 -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_schaefer400x7_names.1D -o /out/sub-01/ses-01/roiquant/schaefer400x7/sub-01_ses-01_schaefer400x7_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -x /xcpEngine/atlas/global/globalNodeIndex.1D -n /xcpEngine/atlas/global/globalNodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -n global -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_alff-quantifyAtlas_global_mean.1D -a anatomical_alff_mean_global -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -n global -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_alffZ-quantifyAtlas_global_mean.1D -a anatomical_alffZ_mean_global -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -n global -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_reho-quantifyAtlas_global_mean.1D -a anatomical_reho_mean_global -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -n global -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_global.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_mean_rehoZ-quantifyAtlas_global_mean.1D -a anatomical_rehoZ_mean_global -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_global_names.1D -o /out/sub-01/ses-01/roiquant/global/sub-01_ses-01_global_mean_rehoZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -x /xcpEngine/atlas/segmentation3/segmentation3NodeIndex.1D -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_alff.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_alff -d anatomical_alff -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -n segmentation -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_alff-quantifyAtlas_segmentation_mean.1D -a anatomical_alff_mean_segmentation -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_alff.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_alffZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_alffZ -d anatomical_alffZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -n segmentation -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -nzmean /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_alffZ-quantifyAtlas_segmentation_mean.1D -a anatomical_alffZ_mean_segmentation -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_alffZ.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_reho.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_reho -d anatomical_reho -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -n segmentation -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_reho-quantifyAtlas_segmentation_mean.1D -a anatomical_reho_mean_segmentation -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_reho.csv -p sub-01,ses-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -s mean -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_rehoZ.csv -t /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_rehoZ -d anatomical_rehoZ -a /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -n segmentation -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -r /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -p sub-01,ses-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_idx.1D -mask /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz -nzmean /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /out/sub-01/ses-01/sub-01_ses-01_atlas/sub-01_ses-01_segmentation.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> ${XCPEDIR}/utils/rs2rq.R -i /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_mean_rehoZ-quantifyAtlas_segmentation_mean.1D -a anatomical_rehoZ_mean_segmentation -n /tmp/sub-01_ses-01-roiquant-421240507~TEMP~_segmentation_names.1D -o /out/sub-01/ses-01/roiquant/segmentation/sub-01_ses-01_segmentation_mean_rehoZ.csv -p sub-01,ses-01

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

                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/sub-01_ses-01.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/alff/sub-01_ses-01_alff.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_alffStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_alffZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/alff/sub-01_ses-01_alffZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_alffZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/alff/sub-01_ses-01_alff_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_alff_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/regress/sub-01_ses-01_img_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_img_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/prestats/sub-01_ses-01_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_maskStd.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/prestats/sub-01_ses-01_referenceVolumeBrain.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/reho/sub-01_ses-01_reho.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_rehoStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_rehoZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/reho/sub-01_ses-01_rehoZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_rehoZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/reho/sub-01_ses-01_reho_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /out/sub-01/ses-01/norm/sub-01_ses-01_reho_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz -bin /tmp/sub-01_ses-01-norm-646595680~TEMP~-seq2std_mask.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /tmp/sub-01_ses-01-norm-646595680~TEMP~-seq2std_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/regslicer -s /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz -t /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -i /tmp/sub-01_ses-01-norm-646595680~TEMP~ -o /out/sub-01/ses-01/norm/sub-01_ses-01_seq2std
                             -   -   -
>> slicer /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -s 2 -x 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sla.png -x 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slb.png -x 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slc.png -x 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sld.png -y 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sle.png -y 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slf.png -y 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slg.png -y 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slh.png -z 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sli.png -z 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slj.png -z 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slk.png -z 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sll.png
                             -   -   -
>> pngappend /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sla.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slb.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slc.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sld.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sle.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slf.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slg.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slh.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sli.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slj.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slk.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sll.png /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_source2target1.png
                             -   -   -
>> slicer /xcpEngine/space/MNI/MNI-2x2x2.nii.gz /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz -s 2 -x 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sla.png -x 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slb.png -x 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slc.png -x 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sld.png -y 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sle.png -y 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slf.png -y 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slg.png -y 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slh.png -z 0.35 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sli.png -z 0.45 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slj.png -z 0.55 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slk.png -z 0.65 /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sll.png
                             -   -   -
>> pngappend /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sla.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slb.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slc.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sld.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sle.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slf.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slg.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slh.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sli.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slj.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_slk.png + /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_sll.png /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_source2target2.png
                             -   -   -
>> pngappend /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_source2target1.png - /tmp/sub-01_ses-01-norm-646595680~TEMP~-regslicer_source2target2.png /out/sub-01/ses-01/norm/sub-01_ses-01_seq2std.png

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

                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/layerLabels -l /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -i /tmp/sub-01_ses-01-qcfc-089387089~TEMP~ -o /out/sub-01/ses-01/qcfc/sub-01_ses-01_depthMap.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -thr 1 -uthr 1 -div 1 -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> ImageMath 3 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz MaurerDistance /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz -mul /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz -m /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz -o /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz -mul 100 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz -mul 100 -add /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-1.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -thr 2 -uthr 2 -div 2 -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> ImageMath 3 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz MaurerDistance /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz -mul /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz -m /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz -o /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz -mul 200 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz -mul 100 -add /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-2.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/prestats/sub-01_ses-01_segmentation.nii.gz -thr 3 -uthr 3 -div 3 -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> ImageMath 3 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz MaurerDistance /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz -sub 1 -mul -1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz -mul /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz -m /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz -o /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz -mul 300 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz -mul 100 -add /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-class-3.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-1.nii.gz -add /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-2.nii.gz -add /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-layerLabels-depth-3.nii.gz /out/sub-01/ses-01/qcfc/sub-01_ses-01_depthMap.nii.gz
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-pp-rs.nii.gz -inset /out/sub-01/ses-01/prestats/sub-01_ses-01_preprocessed.nii.gz -rmode Li
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dn-rs.nii.gz -inset /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dn.nii.gz -rmode Li
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dn.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-onion-rs.nii.gz -inset /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-onion.nii.gz -rmode NN
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-onion.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
                             -   -   -
>> fslval /data/sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/voxts.R -i /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-pp-rs.nii.gz,/tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dn-rs.nii.gz -r /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-onion-rs.nii.gz -o /out/sub-01/ses-01/qcfc/sub-01_ses-01_voxts.png -t DV:/tmp/sub-01_ses-01-qcfc-089387089~TEMP~_dvar.1D:1.5,RMS:/tmp/sub-01_ses-01-qcfc-089387089~TEMP~_rms1.1D:.249000000,FD:/tmp/sub-01_ses-01-qcfc-089387089~TEMP~_fd.1D:.501000000 -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /out/sub-01/ses-01/norm/sub-01_ses-01_referenceVolumeBrainStd.nii.gz -r /out/sub-01/ses-01/prestats/sub-01_ses-01_struct.nii.gz -o /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-referenceVolumeBrain.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -o /out/sub-01/ses-01/qcfc/sub-01_ses-01_dvars -s /tmp/sub-01_ses-01-qcfc-089387089~TEMP~ -d 1 -b /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -Tperc 25 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-lowerQuartile.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -Tperc 75 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-upperQuartile.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-upperQuartile.nii.gz -sub /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-lowerQuartile.nii.gz -div 1.34897950039 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-temporalSD.nii.gz
                             -   -   -
>> fslmaths /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz -Tar1 /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-temporalAR.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-temporalAR.nii.gz -mul -1 -add 1 -mul 2 -sqrt -mul /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-temporalSD.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-predictedSD.nii.gz
                             -   -   -
>> fslstats /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-predictedSD.nii.gz -k /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> fslnvols /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz
                             -   -   -
>> fslroi /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t-1.nii.gz 0 199
                             -   -   -
>> fslroi /out/sub-01/ses-01/regress/sub-01_ses-01_residualised.nii.gz /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t.nii.gz 1 200
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t-1.nii.gz -sqr /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-tdiff-sq.nii.gz
                             -   -   -
>> fslmaths /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t.nii.gz -sub /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-t-1.nii.gz -div /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-predictedSD.nii.gz -sqr /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-tdiff-vox-std.nii.gz
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-tdiff-sq.nii.gz -k /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> fslstats -t /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-dvars-tdiff-vox-std.nii.gz -k /tmp/sub-01_ses-01-qcfc-089387089~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /out/sub-01/ses-01/qcfc/sub-01_ses-01_dvars-std.1D -o mean -f /out/sub-01/ses-01/qcfc/sub-01_ses-01_dvars-mean.txt
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /out/sub-01/ses-01/qcfc/sub-01_ses-01_dvars-std.1D,/tmp/sub-01_ses-01-qcfc-089387089~TEMP~_rms.1D