################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ XCP ENGINE LOCALISER ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### Current processing step: @1 Localising subject metadata... ···································································· · @1.1 [Parsing subject identifiers] · @1.1a [Creating output directory] · @1.1b [/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001] · @1.2 [Initialising space mapping] · @1.2.1 [Native space: TNI.SC.1.002_T001_fc] · @1.2.2a [Standard space: MNI] · @1.2.2c [Loading space: OASIS] · @1.2.3a [Anatomical space: TNI.SC.1.002_T001_anatomical] · @u.2 · @u.2.1 · @u.3 · @u.3.1 · @u.3.1 · @u.3.2 · @u.3.3 · @u.3.3 · @u.3.4 · @u.5 · @u.6 · @1.3 [Initialising derivative maps] · @1.4 [Initialising atlas system] · @1.5 [Priming analytic audit] · @1.6 [Priming quality assessment] ···································································· Processing step complete: Localising subject metadata... Current processing step: @2 Localising image ···································································· · @2.1 [Verifying that images are present] · @2.2 [Conforming and localising images] - - - >> fslchfiletype NIFTI_GZ /data/jag/jmedaglia/TNI_study/Data/RealStim/TNI.SC.1.002/Pre/TNI.SC.1.002_restingBOLD_mb6_1200_20170215152154_10.nii /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz ···································································· Processing step complete: Localising image Current processing step: @3 Localising design ···································································· · @3.1 [Writing localised design] · @3.2 [Evaluating subject variables] ···································································· Processing step complete: Localising design Localiser complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ FMRI PREPROCESSING MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats] - - - >> 0.083*0.500000 - - - >> 0.167*0.500000 prestats has already run to completion. Writing outputs... - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_preprocessed.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz Module Workflow Map ···································································· · START · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ IMAGE COREGISTRATION MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/coreg] - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_meanIntensityBrain.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/coreg/TNI.SC.1.002_T001_source.nii.gz - - - >> ln -sf /data/picsl/akelkar/TNIACToutput_OASIStemplate/TNI.SC.1.002/TNIExtractedBrain0N4.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/coreg/TNI.SC.1.002_T001_target.nii.gz - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/coreg/TNI.SC.1.002_T001~TEMP~.nii.gz Current processing step: @3 Obtaining voxelwise weights ···································································· · @3.2 [Structural: all voxels weighted uniformly] · @3.4 [Input: all voxels weighted uniformly] ···································································· Processing step complete: Obtaining voxelwise weights Current processing step: @4 Executing affine coregistration ···································································· · @4.3 [Coregistration already run] ···································································· Processing step complete: Executing affine coregistration Current processing step: @8 Derivative transformations ···································································· ···································································· Processing step complete: Derivative transformations · @0.1 Module Workflow Map ···································································· · START · @3 · @3.2 · @3.4 · @4 · @4.3 · @8 · @0.1 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ CONFOUND MODEL MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound] Current processing step: @0 Generating confound matrix ···································································· · @1 [Including realignment parameters] - - - >> ${XCPEDIR}/utils/mbind.R -x null -y /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/mc/TNI.SC.1.002_T001_realignment_proc.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D · @3.10 · @3 [Including cerebrospinal fluid signal] · @3.3 - - - >> fslmeants -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_csf.1D -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_csfMask.nii.gz - - - >> ${XCPEDIR}/utils/mbind.R -x /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D -y /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_csf.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D · @3 [Including white matter signal] · @3.3 - - - >> fslmeants -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_wm.1D -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_wmMask.nii.gz - - - >> ${XCPEDIR}/utils/mbind.R -x /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D -y /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_wm.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D · @4 [Global/local signals] · @4.1 · @4.3 Including mean global signal - - - >> fslmeants -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_gsr -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_mask.nii.gz - - - >> ${XCPEDIR}/utils/mbind.R -x /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D -y /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001~TEMP~_phys_gsr -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D · @6 [Including 1 derivative(s)] - - - >> ${XCPEDIR}/utils/mbind.R -x /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D -y OPdx1 -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D · @7 [Including 2 power(s)] - - - >> ${XCPEDIR}/utils/mbind.R -x /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D -y OPpower2 -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_confmat.1D - - - >> fslnvols /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz ···································································· Processing step complete: Generating confound matrix Current processing step: @11 Validating confound model ···································································· · @11.1a [Expected confounds: 36] · @11.1b [Observed confounds: 36] · @11.1 [Confound matrix dimensions validated] - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/confound/TNI.SC.1.002_T001_modelParameterCount.txt ···································································· Processing step complete: Validating confound model Module Workflow Map ···································································· · START · @0 · @1 · @3.10 · @3 · @3.3 · @3 · @3.3 · @4 · @4.1 · @4.3 · @6 · @7 · @11 · @11.1a · @11.1b · @11.1 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ CONFOUND REGRESSION MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/regress] - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/regress/TNI.SC.1.002_T001~TEMP~.nii.gz Current processing step: @6 Spatially filtering image ···································································· · @6.1 · @6.2 [Configuring SUSAN] · @6.4 · @6.6 · @6.7b ···································································· Processing step complete: Spatially filtering image - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/regress/TNI.SC.1.002_T001_residualised.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz Module Workflow Map ···································································· · START · @6 · @6.1 · @6.2 · @6.4 · @6.6 · @6.7b · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ FUNCTIONAL CONNECTOME MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon] - - - >> rm -rf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/TNI.SC.1.002_T001~TEMP~* · @0.1 - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_referenceVolume.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/TNI.SC.1.002_T001_referenceVolume.nii.gz Current processing step: @1 Functional connectome: power264 ···································································· · @1.2 Mapping network to image space · @1.2.2 - - - >> fslstats /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264MNI.nii.gz -R - - - >> 264.000000<=1 - - - >> antsApplyTransforms -e 3 -d 3 -i /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264MNI.nii.gz -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_meanIntensityBrain.nii.gz -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -n MultiLabel -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/coreg/TNI.SC.1.002_T001_struct2seq.txt -t /data/picsl/akelkar/TNIACToutput_OASIStemplate/TNI.SC.1.002/TNITemplateToSubject1GenericAffine.mat -t /data/picsl/akelkar/TNIACToutput_OASIStemplate/TNI.SC.1.002/TNITemplateToSubject0Warp.nii.gz -t /data/jag/jmedaglia/software/xcp/xcpEngine/space/OASIS/OASIS_transforms/MNI-OASIS_1Affine.mat -t /data/jag/jmedaglia/software/xcp/xcpEngine/space/OASIS/OASIS_transforms/MNI-OASIS_0Warp.nii.gz - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264.nii.gz · @1.3 Computing network timeseries - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_ts.1D - - - >> ${XCPEDIR}/utils/roi2ts.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -l /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264NodeIndex.1D · @1.4 Computing adjacency matrix - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264.net - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_missing.txt - - - >> ${XCPEDIR}/utils/ts2adjmat.R -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_ts.1D - - - >> ${XCPEDIR}/utils/adjmat2pajek.R -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -t N · @1.5 Determining node coverage - - - >> ${XCPEDIR}/utils/missingIdx.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt · @1.6 Computing dynamic connectome · @1.6.1 Window: 10 TRs - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_tsEdge.1D - - - >> ${XCPEDIR}/utils/mtd.R -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_ts.1D -w 10 -p FALSE ···································································· Processing step complete: Functional connectome: power264 Module Workflow Map ···································································· · START · @0.1 · @1 · @1.2 · @1.2.2 · @1.3 · @1.4 · @1.5 · @1.6 · @1.6.1 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ REGIONAL HOMOGENEITY MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho] - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_referenceVolume.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_referenceVolume.nii.gz · @0.1 Module Workflow Map ···································································· · START · @0.1 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ AMPLITUDE OF LOW-FREQUENCY FLUCTUATIONS MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff] - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_referenceVolume.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_referenceVolume.nii.gz Current processing step: @1 Spatially filtering image ···································································· · @1.1 · @1.2 [Configuring SUSAN] · @1.4 · @1.6 · @1.7a ···································································· Processing step complete: Spatially filtering image Current processing step: @2 Amplitude of low-frequency fluctuations ···································································· · @2.0 At smoothness 0 mm · @2.0 At smoothness 6 mm ···································································· Processing step complete: Amplitude of low-frequency fluctuations · @0.1 Module Workflow Map ···································································· · START · @1 · @1.1 · @1.2 · @1.4 · @1.6 · @1.7a · @2 · @2.0 · @2.0 · @0.1 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ NETWORK ANALYSIS MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net] - - - >> rm -rf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/TNI.SC.1.002_T001~TEMP~* · @0.1 Current processing step: @1 Network analysis: power264 ···································································· - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264 · @1.1.1 Detecting community structure - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1 · @1.1.2 - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/thirdparty/')) - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/utils/')) - - - >> matlab : glconsensusCL('/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt','/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1/TNI.SC.1.002_T001_CommunityPartitionRes1','gamma',1,'nreps',1) - - - >> matlab : exit - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5 · @1.1.2 - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/thirdparty/')) - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/utils/')) - - - >> matlab : glconsensusCL('/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt','/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5/TNI.SC.1.002_T001_CommunityPartitionRes1x5','gamma',1.5,'nreps',1) - - - >> matlab : exit - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7 · @1.1.2 - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/thirdparty/')) - - - >> matlab : addpath(genpath('/data/jag/jmedaglia/software/xcp/xcpEngine/utils/')) - - - >> matlab : glconsensusCL('/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt','/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7/TNI.SC.1.002_T001_CommunityPartitionRes7','gamma',7,'nreps',1) - - - >> matlab : exit · @1.2 Computing community statistics · @1.2.1 - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionAPriori · @1.2.2 - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionAPriori/TNI.SC.1.002_T001_CommunityPartitionAPriori_modularity.txt - - - >> ${XCPEDIR}/utils/quality.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264CommunityAffiliation.1D - - - >> ${XCPEDIR}/utils/withinBetween.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264CommunityAffiliation.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionAPriori/TNI.SC.1.002_T001_CommunityPartitionAPriori · @1.2.1 - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1 · @1.2.2 - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1/TNI.SC.1.002_T001_CommunityPartitionRes1_modularity.txt - - - >> ${XCPEDIR}/utils/quality.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1/TNI.SC.1.002_T001_CommunityPartitionRes1_partition.1D - - - >> ${XCPEDIR}/utils/withinBetween.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1/TNI.SC.1.002_T001_CommunityPartitionRes1_partition.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1/TNI.SC.1.002_T001_CommunityPartitionRes1 · @1.2.1 - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5 · @1.2.2 - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5/TNI.SC.1.002_T001_CommunityPartitionRes1x5_modularity.txt - - - >> ${XCPEDIR}/utils/quality.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5/TNI.SC.1.002_T001_CommunityPartitionRes1x5_partition.1D - - - >> ${XCPEDIR}/utils/withinBetween.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5/TNI.SC.1.002_T001_CommunityPartitionRes1x5_partition.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes1x5/TNI.SC.1.002_T001_CommunityPartitionRes1x5 · @1.2.1 - - - >> mkdir -p /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7 · @1.2.2 - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7/TNI.SC.1.002_T001_CommunityPartitionRes7_modularity.txt - - - >> ${XCPEDIR}/utils/quality.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7/TNI.SC.1.002_T001_CommunityPartitionRes7_partition.1D - - - >> ${XCPEDIR}/utils/withinBetween.R -m /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/fcon/power264/TNI.SC.1.002_T001_power264_network.txt -c /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7/TNI.SC.1.002_T001_CommunityPartitionRes7_partition.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/net/power264/CommunityPartitionRes7/TNI.SC.1.002_T001_CommunityPartitionRes7 ···································································· Processing step complete: Network analysis: power264 Module Workflow Map ···································································· · START · @0.1 · @1 · @1.1.1 · @1.1.2 · @1.1.2 · @1.1.2 · @1.2 · @1.2.1 · @1.2.2 · @1.2.1 · @1.2.2 · @1.2.1 · @1.2.2 · @1.2.1 · @1.2.2 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ ATLAS-BASED QUANTIFICATION MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant] · @0.1 - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_referenceVolume.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001_referenceVolume.nii.gz - - - >> fslstats /data/picsl/akelkar/TNIACToutput_OASIStemplate/TNI.SC.1.002/TNIBrainSegmentation.nii.gz -R Current processing step: @1 Regional quantification: power264 ···································································· · @1.2 Mapping network to image space · @1.2.1 · @1.2.7 - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264.nii.gz · @1.3.3 - - - >> ${XCPEDIR}/utils/nodeCoverage.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_mask.nii.gz -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -x /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264NodeIndex.1D -n /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/power264/power264NodeNames.txt · @1.3.4 Computing atlas statistics - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alff.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_alff.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_mean_alff -d fc_alff -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -n power264 -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alffZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_alffZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_mean_alffZ -d fc_alffZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -n power264 -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_reho.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_reho.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_mean_reho -d fc_reho -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -n power264 -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_rehoZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_rehoZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_mean_rehoZ -d fc_rehoZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_power264.nii.gz -n power264 -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_power264_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> atlas_set power264 RegionalMeanAlff /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_alff.csv - - - >> atlas_set power264 RegionalMeanAlffZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_alffZ.csv - - - >> atlas_set power264 RegionalMeanReho /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_reho.csv - - - >> atlas_set power264 RegionalMeanRehoZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/power264/TNI.SC.1.002_T001_power264_mean_rehoZ.csv · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 ···································································· Processing step complete: Regional quantification: power264 Current processing step: @1 Regional quantification: global ···································································· · @1.2 Mapping network to image space · @1.2.1 · @1.2.7 - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global.nii.gz · @1.3.3 - - - >> ${XCPEDIR}/utils/nodeCoverage.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_mask.nii.gz -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -x /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/global/globalNodeIndex.1D -n /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/global/globalNodeNames.txt Error in file(file, "rt") : cannot open the connection Calls: as.vector -> unlist -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/data/jag/jmedaglia/software/xcp/xcpEngine/atlas/global/globalNodeIndex.1D': No such file or directory Execution halted · @1.3.4 Computing atlas statistics - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alff.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alff.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_alff -d fc_alff -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -n global -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -p TNI.SC.1.002,T001 -w 0 · @u.1 Mean fc alff over global - - - >> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -mask /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -nzmean /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alff.nii.gz · @u.8 - - - >> ${XCPEDIR}/utils/rs2rq.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_alff-quantifyAtlas_global_mean.1D -a fc_alff_mean_global -n /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alff.csv -p TNI.SC.1.002,T001 Error in read.table(input, header = T) : no lines available in input Execution halted - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alffZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alffZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_alffZ -d fc_alffZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -n global -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -p TNI.SC.1.002,T001 -w 0 · @u.1 Mean fc alffZ over global - - - >> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -mask /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -nzmean /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alffZ.nii.gz · @u.8 - - - >> ${XCPEDIR}/utils/rs2rq.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_alffZ-quantifyAtlas_global_mean.1D -a fc_alffZ_mean_global -n /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alffZ.csv -p TNI.SC.1.002,T001 Error in read.table(input, header = T) : no lines available in input Execution halted - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_reho.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_reho.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_reho -d fc_reho -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -n global -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -p TNI.SC.1.002,T001 -w 0 · @u.1 Mean fc reho over global - - - >> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -mask /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -nzmean /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_reho.nii.gz · @u.8 - - - >> ${XCPEDIR}/utils/rs2rq.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_reho-quantifyAtlas_global_mean.1D -a fc_reho_mean_global -n /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_reho.csv -p TNI.SC.1.002,T001 Error in read.table(input, header = T) : no lines available in input Execution halted - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_rehoZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_rehoZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_rehoZ -d fc_rehoZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -n global -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -p TNI.SC.1.002,T001 -w 0 · @u.1 Mean fc rehoZ over global - - - >> 3dROIstats -1DRformat -nomeanout -nobriklab -roisel /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_idx.1D -mask /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_global.nii.gz -nzmean /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_rehoZ.nii.gz · @u.8 - - - >> ${XCPEDIR}/utils/rs2rq.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_mean_rehoZ-quantifyAtlas_global_mean.1D -a fc_rehoZ_mean_global -n /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_global_names.1D -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_rehoZ.csv -p TNI.SC.1.002,T001 Error in read.table(input, header = T) : no lines available in input Execution halted - - - >> atlas_set global RegionalMeanAlff /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alff.csv - - - >> atlas_set global RegionalMeanAlffZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_alffZ.csv - - - >> atlas_set global RegionalMeanReho /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_reho.csv - - - >> atlas_set global RegionalMeanRehoZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/global/TNI.SC.1.002_T001_global_mean_rehoZ.csv · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 ···································································· Processing step complete: Regional quantification: global Current processing step: @1 Regional quantification: segmentation ···································································· · @1.2 Mapping network to image space · @1.2.1 · @1.2.7 - - - >> ln -sf /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation.nii.gz · @1.3.3 - - - >> ${XCPEDIR}/utils/nodeCoverage.R -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/prestats/TNI.SC.1.002_T001_mask.nii.gz -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz -x /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/segmentation6/segmentation6NodeIndex.1D -n /data/jag/jmedaglia/software/xcp/xcpEngine/atlas/segmentation6/segmentation6NodeNames.txt · @1.3.4 Computing atlas statistics - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alff.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_alff.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_mean_alff -d fc_alff -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz -n segmentation -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/alff/TNI.SC.1.002_T001_alffZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_alffZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_mean_alffZ -d fc_alffZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz -n segmentation -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_reho.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_reho.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_mean_reho -d fc_reho -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz -n segmentation -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> ${XCPEDIR}/utils/quantifyAtlas -v /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/reho/TNI.SC.1.002_T001_rehoZ.nii.gz -s mean -o /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_rehoZ.csv -t /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_mean_rehoZ -d fc_rehoZ -a /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001_atlas/TNI.SC.1.002_T001_segmentation.nii.gz -n segmentation -i /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_idx.1D -r /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/TNI.SC.1.002_T001~TEMP~_segmentation_names.1D -p TNI.SC.1.002,T001 -w 0 [already complete] - - - >> atlas_set segmentation RegionalMeanAlff /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_alff.csv - - - >> atlas_set segmentation RegionalMeanAlffZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_alffZ.csv - - - >> atlas_set segmentation RegionalMeanReho /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_reho.csv - - - >> atlas_set segmentation RegionalMeanRehoZ /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/roiquant/segmentation/TNI.SC.1.002_T001_segmentation_mean_rehoZ.csv · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 ···································································· Processing step complete: Regional quantification: segmentation Module Workflow Map ···································································· · START · @0.1 · @1 · @1.2 · @1.2.1 · @1.2.7 · @1.3.3 · @1.3.4 · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 · @1 · @1.2 · @1.2.1 · @1.2.7 · @1.3.3 · @1.3.4 · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 · @1 · @1.2 · @1.2.1 · @1.2.7 · @1.3.3 · @1.3.4 · @1.3.5 · @1.3.6 · @1.3.7 · @1.3.8 · FINISH ···································································· Module complete ################################################################### # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # # # # ☭ FUNCTIONAL QUALITY ASSESSMENT MODULE ☭ # # # # ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ ☭ # ################################################################### [I][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/TNI.SC.1.002_T001.nii.gz] [O][/data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/qcfc] /data/jag/jmedaglia/software/xcp/xcpEngine/core/functions/rerun: line 3: == 1 : syntax error: operand expected (error token is "== 1 ") /data/jag/jmedaglia/software/xcp/xcpEngine/core/functions/rerun: line 3: == 1 : syntax error: operand expected (error token is "== 1 ") /data/jag/jmedaglia/software/xcp/xcpEngine/core/functions/rerun: line 3: == 1 : syntax error: operand expected (error token is "== 1 ") Current processing step: @4 Estimating loss of temporal degrees of freedom ···································································· - - - >> rm -f /data/jag/jmedaglia/TNI_study/rsfmriPreproc/output/TNI.SC.1.002/T001/qcfc/TNI.SC.1.002_T001_tdof.txt · @4.1 36 nuisance parameters regressed · @4.4 Total lost tDOF: 36 ···································································· Processing step complete: Estimating loss of temporal degrees of freedom /data/jag/jmedaglia/software/xcp/xcpEngine/core/functions/rerun: line 3: == 1 : syntax error: operand expected (error token is "== 1 ") Module Workflow Map ···································································· · START · @4 · @4.1 · @4.4 · FINISH ···································································· /data/jag/jmedaglia/software/xcp/xcpEngine/core/functions/cleanup: line 3: == 1 : syntax error: operand expected (error token is "== 1 ") Module complete