Seedconnectivity Via Singularity Stopped Working

[AlexandraBatzdorf]

EDIT: This was resolved by including --cleanenv in my singularity call.

Describe the bug

I was trying to run seedconnectivity via Singularity, which has worked previously. When it checks if the input and output exist and calls FSL, it says, “no such file or directory.” Perhaps relatedly, I now get an info message telling me that SINGULARITY_TMPDIR is set, but APPTAINER_TMPDIR is preferred.

The script I ran:

#!/bin/bash

# Seed example: RAmygdala

fullseed=${1}
extstrip=".nii.gz"
seed=${fullseed//$extstrip/} # if the seed name contains .nii.gz, remove the file extension
maskdir=../../../rois
maskfile=${maskdir}/${seed}.nii.gz

outdir_base=~/analysis/data/resting/seed_connectivity/scan_level_maps

xcp_dir=~/data/derivatives/xcp-rest
xcp_utils=~/software/xcp/xcpEngine/utils

for scandir in ${xcp_dir}/sub-*/ses-*/task-*; do
        sub=$(echo ${scandir} | awk -F '/' '{print $(NF-2)}')
        ses=$(echo ${scandir} | awk -F '/' '{print $(NF-1)}')
        scan=$(basename ${scandir})

                echo
                echo "${sub} - ${ses} - ${scan}"
                echo

                if [ ! -f ${outdir_base}/${sub}/${ses}/${scan}/seed/${seed}/_connectivity_${seed}Z_sm0.nii.gz  ]; then
                        if [ -f ${scandir}/regress/${sub}_${ses}_${scan}_img_sm6.nii.gz ]; then
                                singularity exec ~/software/singularity/xcpEngine-1.1.0.simg ${xcp_utils}/seedconnectivity \
                                        -i ${scandir}/regress/${sub}_${ses}_${scan}_img_sm6.nii.gz \
                                        -s ${maskfile} \
                                        -o ${outdir_base}/${sub}/${ses}/${scan} \
                                        -n ${seed}
                        fi
                else
                        echo "The ${sub}-${ses}-${scan} scan was already processed by the seedconnectivity XCP utility for the ${seed}"
                fi
done

Cohort file

id0, id1,img
sub-018,ses-01,task-rest_dir-PA_run-002,derivatives/fmriprep/sub-018/ses-01/func/sub-018_ses-01_task-rest_dir-PA_run-002_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

Design File

fc-36p_despike.dsn

#!/usr/bin/env bash

###################################################################
#  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  b  #
###################################################################

###################################################################
# An exact copy of the fc-36pdespike.dsn design file from BBL's
# github page, with two exceptions:
# (1) rerun set to 0 for all modules
# (2) norm module has been cut
###################################################################

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

analysis=fc_$(whoami)
design=/data/scripts/preproc/xcp-rest/designs/fc-36p_despike.dsn
sequence=anatomical
standard=MNI%2x2x2

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

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,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]=0
confound2_censor_contig[2]=0
confound2_framewise[2]=fds:0.167,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]=1
regress_cleanup[3]=1
regress_process[3]=DMT-DSP-TMP-REG

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

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
fcon_thr[4]=N
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]=all
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

##################################################################
# 8 QCFC
###################################################################
qcfc_atlas[8]=all
qcfc_sig[8]=fdr
qcfc_rerun[8]=0
qcfc_cleanup[8]=1

Error message

sub-018 - ses-01 - task-rest_dir-PA_run-002

INFO:    Environment variable SINGULARITY_TMPDIR is set, but APPTAINER_TMPDIR is preferred
· check if the input and output exist
/xcpEngine/core/functions/exec_fsl: line 4: /cbica/software/external/fsl/centos7/5.0.11/bin/fslnvols: No such file or directory
/cbica/projects/tmsbp/software/xcp/xcpEngine/utils/seedconnectivity: line 145: / 2: syntax error: operand expected (error token is "/ 2")
/xcpEngine/core/functions/exec_fsl: line 4: /cbica/software/external/fsl/centos7/5.0.11/bin/fslroi: No such file or directory
/xcpEngine/core/functions/exec_fsl: line 4: /cbica/software/external/fsl/centos7/5.0.11/bin/fslmaths: No such file or directory
../../../rois/RAmygdala.nii.gz
· Transforming coordinates to image
/xcpEngine/core/functions/is_image: line 2: /cbica/software/external/fsl/centos7/5.0.11/bin/imtest: No such file or directory
/xcpEngine/core/functions/is_image: line 2: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
___________________________________________________________________
Usage: coor2niffti -i <input> -o <output> <options>
coor2nifti receives an octothorpe-delimited seed index
  as input and creates a network map image as an output.
Compulsory arguments:
 -i : Input cordinates

 -o : Output network
      The path to the file where the output network will
      be written.
Optional arguments:
 -r : Override radius. If this argument is passed to the
      conversion script, then this radius will take the place
      of any voxel radii defined in the seed library.
 -t : Template image [default MNI 2mm]
      The path to an image file that defines the coordinate
      space used in the seed library.
 -x : Trace
      If this flag is set, then any commands called by the
      coor2map routine will be explicitly printed to the
      console or log.
 -m : mm coordinates
      If this flag is toggled, then input coordinates will be
      treated as mm coordinates rather than voxel coordinates, and
      the image qform and sform will be used to convert them to
      voxel coordinates for seed generation.

· ants registration
· smoothing
· Extracting mean timeseries
Error in readNifti(roipath) :
  Failed to read image from path /cbica/projects/tmsbp/analysis/data/resting/seed_connectivity/scan_level_maps/sub-018/ses-01/task-rest_dir-PA_run-002/seed/RAmygdala/_connectivity_RAmygdala_seed.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/cbica/projects/tmsbp/analysis/data/resting/seed_connectivity/scan_level_maps/sub-018/ses-01/task-rest_dir-PA_run-002/seed/RAmygdala/_connectivity_RAmygdala_seed.nii.gz'
Execution halted
· compute correlation
· fisher transformation

Runtime Information

Singularity.

singularity exec ~/software/singularity/xcpEngine-1.1.0.simg ${xcp_utils}/seedconnectivity \
                                        -i ${scandir}/regress/${sub}_${ses}_${scan}_img_sm6.nii.gz \
                                        -s ${maskfile} \
                                        -o ${outdir_base}/${sub}/${ses}/${scan} \
                                        -n ${seed}

Additional context

N/A

[AlexandraBatzdorf]

PATH issue. This was resolved by including --cleanenv in my singularity call.