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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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empty .net output from possible bug in adjmat2pajek.R #430

Closed mwvoss closed 3 years ago

mwvoss commented 3 years ago

Describe the bug I'm testing xcp v1.2.3 on output from fmriprep v20.1.1 and v1.2.1

Cohort file Paste cohort file between the triple backticks

id0, id1,img

sub-01 | fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-- | --

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

#!/usr/bin/env bash

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the module that
#                  calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are typically array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

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

analysis=fc_$(whoami)
design=/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/code/xcp/fc-aroma.dsn
sequence=anatomical
standard=MNI%2x2x2

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

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

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

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

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

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

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

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

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

fcon_atlas[4]=schaefer400
fcon_metric[4]=corrcoef
fcon_rerun[4]=0
fcon_cleanup[4]=1

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

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

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

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

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

roiquant_atlas[7]=schaefer400
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]=schaefer400
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message Paste your error message between the backticks

>> ${XCPEDIR}/utils/adjmat2pajek.R -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x17/sub-01_schaefer400x17_network.txt -t
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "t" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· @1.5 Determining node coverage

Runtime Information Running with singularity

Additional context Add any other context about the problem here.

a3sha2 commented 3 years ago

pls can you post the logfiles

mwvoss commented 3 years ago

Subject log file:


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

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

                             -   -   -
>> 3dinfo -orient /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01~TEMP~.nii.gz
** AFNI converts NIFTI_datatype=4 (INT16) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01~TEMP~.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.
                             -   -   -
>> 3dinfo -orient /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
                             -   -   -
>> immv /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01~TEMP~ /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01~TEMP~_FMP
                             -   -   -
>> 3dresample -orient LPI -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -overwrite
** AFNI converts NIFTI_datatype=4 (INT16) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_boldref.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.
                             -   -   -
>> antsApplyTransforms -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_structmask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_structmask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz
                             -   -   -
>> antsApplyTransforms -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_structbrain.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> imcp /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz
                             -   -   -
>> fslval /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz -t 2.500000
                             -   -   -
>> 3dresample -orient LPI -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz -overwrite
** AFNI converts NIFTI_datatype=4 (INT16) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.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.

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

                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j stdVARS -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_dvars-std.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j rps -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_realignment.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j fd -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/fd.R -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_realignment.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_fd.1D
                             -   -   -
>> fslstats -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz -S
                             -   -   -
>> 3dTqual -automask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz
++ 3dTqual: AFNI version=AFNI_20.3.01 (Oct 19 2020) [64-bit]
++ Autoclip value = 403.485
++ 48000 out of 251940 voxels survive the clip
++ Median=0.00314701  Median-3.5*MAD=0.000923365  Median+3.5*MAD=0.00537065
                             -   -   -
>> 3dToutcount -automask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz
++ 3dToutcount: AFNI version=AFNI_20.3.01 (Oct 19 2020) [64-bit]
++ 46910 voxels passed mask/clip
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_dvars-std.1D,/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relRMS.1D
                             -   -   -
>> ${XCPEDIR}/utils/tmask.R -s /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01-nFlags.1D -t 0.5 -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_tmask.1D -m 0
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relRMS.1D -o max -f /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relMaxRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relRMS.1D -o mean -f /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/mc/sub-01_relMeanRMS.txt
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j csf -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_csf.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x null -y /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_csf.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j wm -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_wm.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D -y /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_wm.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D
                             -   -   -
>> ${XCPEDIR}/utils/generate_confmat.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_fmriconf.tsv -j aroma -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_aroma.1D
                             -   -   -
>> ${XCPEDIR}/utils/mbind.R -x /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D -y /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_aroma.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D
                             -   -   -
>> fslnvols /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz

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

                             -   -   -
>> ${XCPEDIR}/utils/dmdt.R -d 2 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT.nii.gz -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/1dDMDT.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/confound2/sub-01_confmat.1D -d 2 -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_confmat.1D
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT
                             -   -   -
>> ${XCPEDIR}/utils/tfilter -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP.nii.gz -a 2.500000 -f butterworth -h 0.01 -l 0.08 -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r 1 -d 2 -1 confmat:/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_confmat.1D
                             -   -   -
>> remove_ext /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP.nii.gz
                             -   -   -
>> fslnvols /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT.nii.gz
                             -   -   -
>> fslval /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/genfilter.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP.nii.gz -f butterworth -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -c 0.01 -l 0.08 -r 1 -d 2
                             -   -   -
>> ${XCPEDIR}/utils/1dGenfilter.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_confmat.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_confmat.1D -f butterworth -t 1.000000 -c 0.01 -l 0.08 -r 1 -d 2
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_confmat.1D
                             -   -   -
>> 3dTproject -input /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP.nii.gz -ort /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_confmat.1D -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_REG.nii.gz
++ 3dTproject: AFNI version=AFNI_20.3.01 (Oct 19 2020) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_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
 + -- 15 other fixed ort regressors
++ 105 retained time points MINUS 18 regressors ==> 87 D.O.F. left
++ no -mask option ==> processing all 251940 voxels in dataset
++ Compute pseudo-inverse of fixed orts
++ Loading dataset
*+ WARNING: 3dTproject input data :: 203435 vectors are constant
++ Starting project-orization
++ Convert results to output dataset
++ Output dataset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_REG.nii.gz
++ ===== clock time = 4s 93ms
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_REG /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_REG
                             -   -   -
>> imcp /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01~TEMP~_DMT_TMP_REG.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz
                             -   -   -
>> fslval /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/addTR.py -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -t 2.500000
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz -s susan -k 6 -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -u /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -p 50
                             -   -   -
>> susan /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz 749.51834100000000000000 2.54796540086508437971 3 1 1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz 749.51834100000000000000 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz

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

                             -   -   -
>> fslstats /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -R
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /xcpEngine/atlas/schaefer400x17/schaefer400x17MNI.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -l /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x17/sub-01_schaefer400x17_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x17/sub-01_schaefer400x17_network.txt -t
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x17/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -n MultiLabel -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/roi2ts.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -l /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D
                             -   -   -
>> ${XCPEDIR}/utils/ts2adjmat.R -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x7/sub-01_schaefer400x7_ts.1D
                             -   -   -
>> ${XCPEDIR}/utils/adjmat2pajek.R -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x7/sub-01_schaefer400x7_network.txt -t
                             -   -   -
>> ${XCPEDIR}/utils/missingIdx.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/fcon/schaefer400x7/sub-01_schaefer400x7_network.txt

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

                             -   -   -
>> 3dReHo -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz -nneigh 27
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -M
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -sub 0.161856 -div 0.114517 -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/sfilter -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -s susan -k 6 -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -u /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -p 50
                             -   -   -
>> susan /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz 749.51834100000000000000 2.54796540086508437971 3 1 1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolume.nii.gz 749.51834100000000000000 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -M
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -sub 0.153183 -div 0.087815 -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ_sm6.nii.gz

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

                             -   -   -
>> fslnvols /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz
                             -   -   -
>> fslval /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz pixdim4
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~EVEN.nii.gz 1 104
                             -   -   -
>> fslpspec /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~EVEN.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS.nii.gz -sqrt /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SQRT.nii.gz
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SQRT.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SLOW.nii.gz 2 19
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SLOW.nii.gz -Tmean -mul 19 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -M
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -sub 489.317127 -div 298.005071 -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz
                             -   -   -
>> fslnvols /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz
                             -   -   -
>> fslval /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz pixdim4
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~EVEN.nii.gz 1 104
                             -   -   -
>> fslpspec /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~EVEN.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS.nii.gz -sqrt /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SQRT.nii.gz
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SQRT.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SLOW.nii.gz 2 19
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01~TEMP~PS-SLOW.nii.gz -Tmean -mul 19 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff_sm6.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff_sm6.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -M
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff_sm6.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -S
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff_sm6.nii.gz -sub 237.087036 -div 178.490003 -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ_sm6.nii.gz

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

                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -R
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -x /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeIndex.1D -n /xcpEngine/atlas/schaefer400x17/schaefer400x17NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_alff.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_alff -d anatomical_alff -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -n schaefer400x17 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_alff-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_alff_mean_schaefer400x17 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_alff.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_alffZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_alffZ -d anatomical_alffZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -n schaefer400x17 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_alffZ-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_alffZ_mean_schaefer400x17 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_alffZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_reho.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_reho -d anatomical_reho -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -n schaefer400x17 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_reho-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_reho_mean_schaefer400x17 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_reho.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_rehoZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_rehoZ -d anatomical_rehoZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -n schaefer400x17 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x17.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_mean_rehoZ-quantifyAtlas_schaefer400x17_mean.1D -a anatomical_rehoZ_mean_schaefer400x17 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x17_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x17/sub-01_schaefer400x17_mean_rehoZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -x /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeIndex.1D -n /xcpEngine/atlas/schaefer400x7/schaefer400x7NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_alff.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_alff -d anatomical_alff -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -n schaefer400x7 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_alff-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_alff_mean_schaefer400x7 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_alff.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_alffZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_alffZ -d anatomical_alffZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -n schaefer400x7 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_alffZ-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_alffZ_mean_schaefer400x7 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_alffZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_reho.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_reho -d anatomical_reho -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -n schaefer400x7 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_reho-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_reho_mean_schaefer400x7 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_reho.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_rehoZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_rehoZ -d anatomical_rehoZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -n schaefer400x7 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_schaefer400x7.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_mean_rehoZ-quantifyAtlas_schaefer400x7_mean.1D -a anatomical_rehoZ_mean_schaefer400x7 -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_schaefer400x7_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/schaefer400x7/sub-01_schaefer400x7_mean_rehoZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -x /xcpEngine/atlas/global/globalNodeIndex.1D -n /xcpEngine/atlas/global/globalNodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_alff.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_alff -d anatomical_alff -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -n global -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_alff-quantifyAtlas_global_mean.1D -a anatomical_alff_mean_global -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_alff.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_alffZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_alffZ -d anatomical_alffZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -n global -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_alffZ-quantifyAtlas_global_mean.1D -a anatomical_alffZ_mean_global -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_alffZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_reho.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_reho -d anatomical_reho -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -n global -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_reho-quantifyAtlas_global_mean.1D -a anatomical_reho_mean_global -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_reho.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_rehoZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_rehoZ -d anatomical_rehoZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -n global -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_global.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_mean_rehoZ-quantifyAtlas_global_mean.1D -a anatomical_rehoZ_mean_global -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_global_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/global/sub-01_global_mean_rehoZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/nodeCoverage.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -x /xcpEngine/atlas/segmentation3/segmentation3NodeIndex.1D -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_alff.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_alff -d anatomical_alff -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -n segmentation -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_alff-quantifyAtlas_segmentation_mean.1D -a anatomical_alff_mean_segmentation -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_alff.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_alffZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_alffZ -d anatomical_alffZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -n segmentation -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_alffZ-quantifyAtlas_segmentation_mean.1D -a anatomical_alffZ_mean_segmentation -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_alffZ.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_reho.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_reho -d anatomical_reho -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -n segmentation -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_reho-quantifyAtlas_segmentation_mean.1D -a anatomical_reho_mean_segmentation -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_reho.csv -p sub-01
                             -   -   -
>> ${XCPEDIR}/utils/quantifyAtlas -v /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz -s mean -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_rehoZ.csv -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_rehoZ -d anatomical_rehoZ -a /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -n segmentation -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -p sub-01 -w 0
                             -   -   -
>> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_idx.1D -mask /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-01_segmentation.nii.gz -nzmean /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01_atlas/sub-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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_mean_rehoZ-quantifyAtlas_segmentation_mean.1D -a anatomical_rehoZ_mean_segmentation -n /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/sub-01~TEMP~_segmentation_names.1D -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/roiquant/segmentation/sub-01_segmentation_mean_rehoZ.csv -p sub-01

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

                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/sub-01.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_alffStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_alffZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alffZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_alffZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/alff/sub-01_alff_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_alff_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_img_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_img_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_maskStd.nii.gz -n NearestNeighbor -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_referenceVolumeBrain.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_rehoStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_rehoZStd.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_rehoZ_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_rehoZ_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/reho/sub-01_reho_sm6.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_reho_sm6Std.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz -bin /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-seq2std_mask.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/maskOverlap.R -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-seq2std_mask.nii.gz -r /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/regslicer -s /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz -t /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~ -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_seq2std
                             -   -   -
>> slicer /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz /xcpEngine/space/MNI/MNI-2x2x2.nii.gz -s 2 -x 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sla.png -x 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slb.png -x 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slc.png -x 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sld.png -y 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sle.png -y 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slf.png -y 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slg.png -y 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slh.png -z 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sli.png -z 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slj.png -z 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slk.png -z 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sll.png
                             -   -   -
>> pngappend /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sla.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slb.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slc.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sld.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sle.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slf.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slg.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slh.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sli.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slj.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slk.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sll.png /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_source2target1.png
                             -   -   -
>> slicer /xcpEngine/space/MNI/MNI-2x2x2.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz -s 2 -x 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sla.png -x 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slb.png -x 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slc.png -x 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sld.png -y 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sle.png -y 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slf.png -y 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slg.png -y 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slh.png -z 0.35 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sli.png -z 0.45 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slj.png -z 0.55 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slk.png -z 0.65 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sll.png
                             -   -   -
>> pngappend /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sla.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slb.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slc.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sld.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sle.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slf.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slg.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slh.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sli.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slj.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_slk.png + /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_sll.png /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_source2target2.png
                             -   -   -
>> pngappend /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_source2target1.png - /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01~TEMP~-regslicer_source2target2.png /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_seq2std.png

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

                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/layerLabels -l /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~ -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_depthMap.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -thr 1 -uthr 1 -div 1 -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> ImageMath 3 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz MaurerDistance /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz -mul 100 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz -mul 100 -add /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-1.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -thr 2 -uthr 2 -div 2 -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> ImageMath 3 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz MaurerDistance /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz -mul 200 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz -mul 100 -add /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-2.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_segmentation.nii.gz -thr 3 -uthr 3 -div 3 -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> ImageMath 3 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz MaurerDistance /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz -sub 1 -mul -1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz -m /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz -mul 300 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz -mul 100 -add /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-class-3.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-1.nii.gz -add /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-2.nii.gz -add /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-layerLabels-depth-3.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_depthMap.nii.gz
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-pp-rs.nii.gz -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_preprocessed.nii.gz -rmode Li
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dn-rs.nii.gz -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dn.nii.gz -rmode Li
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-onion-rs.nii.gz -inset /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-onion.nii.gz -rmode NN
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~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 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/fmriprep/fmriprep/sub-01/func/sub-01_task-FlickeringCheckerBoard_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> ${XCPEDIR}/utils/voxts.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-pp-rs.nii.gz,/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dn-rs.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-onion-rs.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_voxts.png -t DV:/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~_dvar.1D:1.5,RMS:/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~_rms1.1D:.207500000,FD:/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~_fd.1D:.417500000 -n /xcpEngine/atlas/segmentation3/segmentation3NodeNames.txt
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/norm/sub-01_referenceVolumeBrainStd.nii.gz -r /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/prestats/sub-01_struct.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-referenceVolumeBrain.nii.gz -t /xcpEngine/utils/oneratiotransform.txt
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -o /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_dvars -s /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~ -d 1 -b /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -Tperc 25 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-lowerQuartile.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -Tperc 75 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-upperQuartile.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-upperQuartile.nii.gz -sub /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-lowerQuartile.nii.gz -div 1.34897950039 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-temporalSD.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz -Tar1 /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-temporalAR.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-temporalAR.nii.gz -mul -1 -add 1 -mul 2 -sqrt -mul /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-temporalSD.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-predictedSD.nii.gz
                             -   -   -
>> fslstats /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-predictedSD.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> fslnvols /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t-1.nii.gz 0 104
                             -   -   -
>> fslroi /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/regress/sub-01_residualised.nii.gz /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t.nii.gz 1 105
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t.nii.gz -sub /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t-1.nii.gz -sqr /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-tdiff-sq.nii.gz
                             -   -   -
>> fslmaths /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t.nii.gz -sub /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-t-1.nii.gz -div /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-predictedSD.nii.gz -sqr /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-tdiff-vox-std.nii.gz
                             -   -   -
>> fslstats -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-tdiff-sq.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> fslstats -t /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-dvars-tdiff-vox-std.nii.gz -k /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_dvars-std.1D -o mean -f /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_dvars-mean.txt
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01_dvars-std.1D,/Shared/vosslabhpc/Projects/CourseData/ds003030/derivatives/xcpOutput_aroma/sub-01/qcfc/sub-01~TEMP~_rms.1D
a3sha2 commented 3 years ago

that is correct. we suppressed .net. you can generate *net from _network.txt

mwvoss commented 3 years ago

Thank you, we have started recreating the *.net from other output. Suggest to not output the empty *.net files in future releases, and suggest how to create the equivalent file in the user documentation.