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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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Error while computing confound correlations using fc-36p_scrub.dsn to do GSR and motion scrubbing #459

Open jli-bwh opened 2 years ago

jli-bwh commented 2 years ago

Describe the bug An error occurred while processing module regress.The error was detected at signpost @4.6

Cohort file Paste cohort file between the triple backticks

id0,id1,img
sub-2001,ses-01,sub-2001/ses-01/func/sub-2001_ses-01_task-rest_run-1_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
sub-2001,ses-01,sub-2001/ses-01/func/sub-2001_ses-01_task-rest_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
sub-2001,ses-01,sub-2001/ses-01/func/sub-2001_ses-01_task-rest_run-3_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz

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

fc-36p_scrub.dsn 

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

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

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

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

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

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=1
confound2_censor_contig[2]=4
confound2_framewise[2]=fds:0.04,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

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

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

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

fcon_atlas[4]=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]=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]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message Paste your error message between the backticks


Current processing step:
Converting BOLD timeseries to confound residuals
····································································
· [Computing confound correlations]
Error in if (any(diag(x) != 0)) stop("Argument 'x' can only have 0s on the diagonal.") : 
  missing value where TRUE/FALSE needed
Calls: squareform
Execution halted
· [Executing detrend]

· [A major error has occurred.]
· [The processing stream will now abort.]
· [Preparing diagnostics]

 [An error occurred while processing module regress.]
· [The error was detected at signpost @4.6.]
· [The most recent command logged was]
· [3dTproject -input /data/nimlab/R01/Butler_fmri_GSR_scrub_0721/sub-2001_ses-01-regress-716279688~TEMP~_DMT.nii.gz -ort /data/nimlab/R01/Butler_fmri_GSR_scrub_0721/sub-2001/ses-01/regress/sub-2001_ses-01_confmat.1D -prefix /data/nimlab/R01/Butler_fmri_GSR_scrub_0721/sub-2001_ses-01-regress-716279688~TEMP~_DMT_REG.nii.gz]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /data/nimlab/R01/Butler_fmri_GSR_scrub_0721/sub-2001_ses-01-regress-716279688~TEMP~_DMT_REG.nii.gz]
· []
· [stream abort]

++ Setting up regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
 + -- 736 other fixed ort regressors
** ERROR: total number of fixed regressors (739) is too many for 700 retained time points!
** FATAL ERROR: Cannot continue after above errors :-( :-( :-( !!
** Program compile date = Apr  9 2021

Runtime Information xcpEngine was run using singularity container fc_jl1003_202107211645_sub-2001_ses-01LOG-process.log

Additional context Add any other context about the problem here.