(cross-post from XCP 1.2.4: fc_acompcor does not proceed to completion · Issue #461 · PennLINC/xcpEngine · GitHub)
Describe the bug
Testing the fc_acompcor pipeline on two Healthy Brain Network subjects’ resting state runs. Same errors come up when trying other fc modules
Cascade of error beginning with the FUNCTIONAL CONNECTOME MODULE
Cohort file
id0,img
sub-NDARAA306NT2,/om4/group/gablab/data/HBN/derivatives/fmriprep/sub-NDARAA306NT2/func/sub-NDARAA306NT2_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
sub-NDARAA948VFH,/om4/group/gablab/data/HBN/derivatives/fmriprep/sub-NDARAA948VFH/func/sub-NDARAA948VFH_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Design File
Copy of the acompcor design
#!/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=/data/jux/BBL/projects/testACT/script/designfiles/fc-acompcor.dsn
design=/om4/group/gablab/data/HBN/code/xcpengine/design_test.dsn
sequence=anatomical
standard=MNI%2x2x2
###################################################################
# PIPELINE
###################################################################
pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc
###################################################################
# 1 PRESTATS
###################################################################
prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP
###################################################################
# 2 CONFOUND2
###################################################################
confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=0
confound2_csf[2]=0
confound2_gsr[2]=0
confound2_acompcor[2]=1
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=1
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_rerun[2]=1
confound2_cleanup[2]=1
###################################################################
# 3 REGRESS
###################################################################
regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_smo[3]=6
regress_sptf[3]=susan
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=1
regress_process[3]=DMT-TMP-REG
###################################################################
# 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
Functional Connectome Module
Current processing step:
Functional connectome: power264
····································································
· Mapping network to image space
· Computing adjacency matrix
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
· Determining node coverage
····································································
Processing step complete:
Functional connectome: power264
Module complete
Functional Quality Assessment Module
Current processing step:
Preparing summary graphics
····································································
· Acquiring arguments
· Generating visuals
Warning messages:
1: Use of `ts$value` is discouraged. Use `value` instead.
2: Use of `ts$value` is discouraged. Use `value` instead.
3: Use of `ts$value` is discouraged. Use `value` instead.
4: Use of `ts$value` is discouraged. Use `value` instead.
5: Use of `ts$value` is discouraged. Use `value` instead.
6: Use of `ts$value` is discouraged. Use `value` instead.
Error: Unequal parameter lengths: x (4), label (3)
Backtrace:
█
1. └─ggplot2::annotate(...)
Execution halted
····································································
Processing step complete:
Preparing summary graphics
Current processing step:
Estimating loss of temporal degrees of freedom
····································································
· 22 nuisance parameters regressed
· 0.8004234 volumes censored
/xcpEngine/modules/qcfc/qcfc.mod: line 247: 22 + 0.8004234 : syntax error: invalid arithmetic operator (error token is ".8004234 ")
/xcpEngine/modules/qcfc/qcfc.mod: line 262: nSpikesDV: command not found
· Total lost tDOF: 22
····································································
Processing step complete:
Estimating loss of temporal degrees of freedom
Group Stage QC
Current processing step:
QC-FC: power264
····································································
· Atlas: power264
· Scanning subject-level atlas metadata
· QC-FC matrix: correlations with motion
Error in cor.test.default(cohort$motion, unlist(unname(cohort[edge]))) :
not enough finite observations
Calls: cor.test -> cor.test.default
Execution halted
mv: cannot stat '/om4/group/gablab/data/HBN/derivatives/xcpengine/group/qcfc/anatomical_QC-FC_correlation_power264_absMedCor.txt': No such file or directory
mv: cannot stat '/om4/group/gablab/data/HBN/derivatives/xcpengine/group/qcfc/anatomical_QC-FC_correlation_power264_nSigEdges.txt': No such file or directory
mv: cannot stat '/om4/group/gablab/data/HBN/derivatives/xcpengine/group/qcfc/anatomical_QC-FC_correlation_power264_pctSigEdges.txt': No such file or directory
· Computing QC-FC distance-dependence
· Estimating distance matrix
· Identifying nodal centres of mass
· Constructing distance matrix
· Computing distance-dependence
····································································
Processing step complete:
QC-FC: power264
Module complete
generating report
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/__init__.py:89: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
"Numpy arrays.", FutureWarning)
Sentry is attempting to send 1 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/__init__.py:89: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
"Numpy arrays.", FutureWarning)
Sentry is attempting to send 1 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit
Runtime Information
Singularity 3.6.3, XCP Contrainer 1.2.4
Additional context
Failed the same way on both subjects.
A lot of outputs are available, but the final fcon adjacency matrices and niftis are not.