Design file not being read (Singularity on CC)

[mgirn]

Describe the bug

XCP is not reading my design file when I run it via Singularity on a Compute Canada computing cluster. Here is the command I'm using:

singularity run \ -B /scratch/maneshg/xcpDenoise:/data \ /scratch/maneshg/xcpDenoise/xcpEngine-latest.simg \ -d /scratch/maneshg/xcpDenoise/data/fc-acompcor.dsn \ -c /scratch/maneshg/xcpDenoise/data/$cohort \ -o /scratch/maneshg/xcpDenoise/derivatives/xcpEngine \ -i /scratch/maneshg/xcpDenoise/derivatives/work_dir \ -r /scratch/maneshg/xcpDenoise/data -t 1 -m c

Cohort file Paste cohort file between the triple backticks

id0, img 
sub-0001, /sub-0001/func/sub-0001_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz

Design File

#!/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=/scratch/maneshg/xcpDenoise/fc-acompcor.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

Received options: -d /scratch/maneshg/xcpDenoise/data/fc-acompcor.dsn -c /scratch/maneshg/xcpDenoise/data/Cohort_1.csv -o /scratch/maneshg/xcpDenoise/derivatives/xcpEngine -i /scratch/maneshg/xcpDenoise/derivatives/work_dir
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D]Missing or empty design file
· [D]Aborting
___________________________________________________________________

Runtime Information

I ran XCP via Singularity on a Compute Canada computing cluster

[a3sha2]

is design file and cohort file in the same directory?

[mgirn]

Yes. They're both in the same directory as the subject data folders.

[a3sha2]

sorry for late response, check if design is free of read and write. To be sure, if the singularity is mounted correctly try the following to see the directory

singularity exec 
-B /scratch/maneshg/xcpDenoise:/data
/scratch/maneshg/xcpDenoise/xcpEngine-latest.simg ls

[mgirn]

What would be the ‘correct’ output from that command? I’m getting the folders in the home directory.

Specifically, the output is:

matlab

nearline

projects

scratch

Also I should mention, a few months ago I had used the exact commands that I’m currently using and it had worked…

From: Azeez Adebimpe @.> Reply-To: PennBBL/xcpEngine @.> Date: Wednesday, March 17, 2021 at 1:34 AM To: PennBBL/xcpEngine @.> Cc: Manesh Girn @.>, Author @.***> Subject: Re: [PennBBL/xcpEngine] Design file not being read (Singularity on CC) (#432)

sorry for late response, check if design is free of read and write. To be sure, if the singularity is mounted correctly try the following to see the directory

singularity exec

-B /scratch/maneshg/xcpDenoise:/data

/scratch/maneshg/xcpDenoise/xcpEngine-latest.simg ls

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[bdeck8317]

@mgirn was there a solution to this issue?

[mgirn]

yes, it was a mounting issue. I can't recall what the exact solution was.