MRIQC not running on CLI

Summary of what happened:

I’m trying to run MRIQC through singularity and it has worked before but its not giving me the result I want now.

My subjects are in the BIDS directory formatted by sub-/ses-/…

I am running in the CLI mriqc_soar.sh SOAR_Mobile 0000201 0110

The script below is supposed to assume sub- and ses- exists before 0000201 and 0110

Command used (and if a helper script was used, a link to the helper script or the command generated):

#!/bin/bash

#SBATCH --time=15:00:00
#SBATCH --nodes=2
#SBATCH --job-name=MRIQC-SOAR
#SBATCH --ntasks=48
#SBATCH --output=/fs/ess/PCON0340/SOAR_Temp/MRI/Scripts/slurm_output/$subject-mriqc-%j.out
#SBATCH --account=PCON0340

site=$1
subject=$2
session=$3

echo "Starting subject" $site $subject $session
echo "Running SOAR script"

singularity run --cleanenv \
/fs/ess/PCON0340/SOAR_Temp/MRI/Scripts/TEST/SOAR_SCRIPTS_PIPELINE/containers/mriqc-24.0.sif \
/fs/ess/PCON0340/SOAR_Temp/MRI/$site/BIDS \
/fs/ess/PCON0340/SOAR_Temp/MRI/$site/MRIQC_2 \
participant \
--participant_label sub-$subject \
--session-id ses-$session \
--work-dir /fs/ess/PCON0340/SOAR_Temp/MRI/$site/MRIQC_2/work \
--verbose-reports


Version:

24.0

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

 *participant_label: ['0000201']
 *session: ['ses-0110']
 *run: None
 *task: None
 *bids_type: None
-bash-4.2$ ./mriqc_soar.sh SOAR_Mobile 0000201 0110
Starting subject SOAR_Mobile 0000201 0110
Running SOAR script
INFO:    underlay of /etc/localtime required more than 50 (103) bind mounts
------------------------------------------------------------------
  Running MRIQC version 24.1.0.dev0+g3fe90466.d20240417
  ----------------------------------------------------------------
  * BIDS dataset path: /fs/ess/PCON0340/SOAR_Temp/MRI/SOAR_Mobile/BIDS.
  * Output folder: /fs/ess/PCON0340/SOAR_Temp/MRI/SOAR_Mobile/MRIQC_2.
  * Analysis levels: ['participant'].
------------------------------------------------------------------

usage: mriqc [-h] [--version] [-v] [--species {human,rat}] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--bids-filter-file PATH] [--session-id [SESSION_ID ...]] [--run-id [RUN_ID ...]]
             [--task-id [TASK_ID ...]] [-m [{T1w,T2w,bold,dwi} ...]] [--dsname DSNAME] [--bids-database-dir PATH] [--bids-database-wipe] [--no-datalad-get] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_GB]
             [--testing] [-f] [--pdb] [-w WORK_DIR] [--verbose-reports] [--reports-only] [--write-graph] [--dry-run] [--resource-monitor] [--use-plugin USE_PLUGIN] [--no-sub] [--email EMAIL] [--webapi-url WEBAPI_URL]
             [--webapi-port WEBAPI_PORT] [--upload-strict] [--notrack] [--ants-float] [--ants-settings ANTS_SETTINGS] [--min-dwi-length MIN_LEN_DWI] [--min-bold-length MIN_LEN_BOLD] [--fft-spikes-detector]
             [--fd_thres FD_THRES] [--deoblique] [--despike] [--start-idx START_IDX] [--stop-idx STOP_IDX]
             bids_dir output_dir {participant,group} [{participant,group} ...]
mriqc: error: Querying BIDS dataset at </fs/ess/PCON0340/SOAR_Temp/MRI/SOAR_Mobile/BIDS> got an empty result.
Please, check out your currently set filters (--bids-filter-file was not set):
{}

Screenshots / relevant information:


Hi @MadhavanSubhashini,

It would help if you could provide the BIDS validation report. But I think your problem will be solved if you bind your drive in Singularity by adding -B /fs/ess/PCON0340/SOAR_Temp/MRI/ after --cleanenv.

Best,
Steven