qcfc.R not creating a anatomical_QC-FC_correlation_ file.

[olawalesalaudeen]

Describe the bug "ERROR: Not all input arguments exist." in anatomical_QC-FC_distanceDependence_schaefer100x17.txt.

It looks like the "${XCPEDIR}/utils/qcfc.R -c /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/~TEMP~-schaefer100-subjects.csv -s fdr -o /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/anatomical_QC-FC_correlation_schaefer100" does not create a "anatomical_QC-FC_correlation_schaefer100" file (can't find it in the output), which causes the error in "${XCPEDIR}/utils/qcfcDistanceDependence -a /xcpEngine/atlas/schaefer100/schaefer100MNI.nii.gz -q /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/anatomical_QC-FC_correlation_schaefer100.txt -o /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/anatomical_QC-FC_distanceDependence_schaefer100.txt -f /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/anatomical_QC-FC_distanceDependence_schaefer100.svg -d /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/anatomical_node_distance_schaefer100.txt -i /tier2/uiuc/oes2/INSIGHT/group_xcpengine_output/group_fc-aroma/qcfc/~TEMP~".

Cohort file Paste cohort file between the triple backticks

id0, id1,img
sub-4001,fc-aroma,/tier2/uiuc/oes2/INSIGHT/fmriprep_output/sub-4001/sub-4001/ses-1/func/sub-4001_ses-1_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
 sub-4004,fc-aroma,/tier2/uiuc/oes2/INSIGHT/fmriprep_output/sub-4004/sub-4004/ses-1/func/sub-4004_ses-1_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
...,...,...

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

#!/usr/bin/env bash

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

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

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

analysis=fc_$(whoami)
design=/xcpEngine/designs/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]=0
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]=schaefer # power264
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]=schaefer # power264
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

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

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

Error message Paste your error message between the backticks

Error message

"ERROR: Not all input arguments exist." in anatomical_QC-FC_distanceDependence_schaefer100x17.txt.

Runtime Information How were you running the software? Docker? Singularity? Directly? If Directly, please consider using Docker or Singluarity first before submitting a bug report.

Singularity.

Additional context Add any other context about the problem here.