Summary of what happened:
I am running fmriprep v23.1.3 and get an error regarding my fmap. I have a phasediff, magnitude1, and magnitude2 json for each participant. In the phasediff json, I have "IntendedFor", "EchoTime1", "EchoTime2", and "B0FieldIdentifier". In each functional json, I have included "B0FieldSource". All json's have "Units": "Hz". It is something to do with the dimensions of the magnitude & phasediff nii.gz but I'm not sure how to further diagnose.
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
#
#$ -cwd
# error = Merged with joblog
#$ -N fmriprep
#$ -o fmriprep_$JOB_ID.out
#$ -j y
#$ -pe shared 2
#$ -l h_rt=24:00:00,h_data=30G
# Email address to notify
#$ -M $EMAIL
# Notify when
#$ -m bea
#$ -t 1-3
#--------------------
# load the job environment:
. /u/local/Modules/default/init/modules.sh
module use /u/project/CCN/apps/modulefiles
module load freesurfer/7.3.2
module load apptainer/1.2.2
GROUP_HOME=/u/project/silvers/data/
BIDS_DIR="${GROUP_HOME}/bids/IR_bids_pipeline/bids_data"
OUTPUT_DIR="${BIDS_DIR}/derivatives/fmriprep-23.1.3"
FREESURFER_DIR="${BIDS_DIR}/derivatives/freesurfer-7.3.2"
# Make sure FS_LICENSE is defined in the container.
export APPTAINERENV_FS_LICENSE=$GROUP_HOME/scripts/containers/license.txt
# Prepare some writeable bind-mount points.
export APPTAINERENV_TEMPLATEFLOW_HOME=$GROUP_HOME/scripts/containers/templateflow
export APPTAINER_HOME="/u/project/CCN/apps/fmriprep/rh7/23.1.3"
export fmriprep="23.1.3-fmriprep.sif"
# setting singularity command
APPTAINER_CMD="apptainer run --cleanenv -B $TMPDIR:/tmp -B $APPTAINERENV_TEMPLATEFLOW_HOME:/templateflow $APPTAINER_HOME/${fmriprep}"
# Parse the participants.tsv file and extract one subject ID from the line corresponding to this SLURM task.
subject=$( sed -n -E "$(($SGE_TASK_ID))s/sub-(\S*)\>.*/\1/gp" ${GROUP_HOME}/bids/IR_bids_pipeline/participants.tsv )
echo $SGE_TASK_ID
# Single sub
#subject= "IRA053"
# Compose the command line
FMRIPREP_OPTS="
--omp-nthreads 8
--nthreads 12
--mem_mb 30000
--skip-bids-validation
--output-spaces MNI152NLin2009cAsym:res-2
--skull-strip-template MNI152NLin2009cAsym
--fs-license-file ${APPTAINERENV_FS_LICENSE}
--fs-subjects-dir ${FREESURFER_DIR}
"
# --fs-no-reconall
# --ignore fieldmaps
# --ignore slicetiming
# --skull-strip-template MNI152NLin6Asym
# --fs-no-reconall
# --omp-nthreads 8
# --nthreads 12
# --mem_mb 30000
# --dummy-scans 6
# --use-aroma
cmd="${APPTAINER_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant --participant-label ${subject} -w /tmp/ -vv ${FMRIPREP_OPTS}"
# Setup done, run the command
echo Running task ${JOB_ID}
echo ${FREESURFER_DIR}/sub-${subject}/scripts/IsRunning*
if [ -e ${FREESURFER_DIR}/sub-${subject}/scripts/IsRunning* ]
then
rmcmd="rm ${FREESURFER_DIR}/sub-${subject}/scripts/IsRunning*"
echo ${rmcmd}
eval ${rmcmd}
fi
echo Commandline: $cmd
eval $cmd
Version:
fmriprep v23.1.3
Environment (Docker, Singularity, custom installation):
Apptainer v1.2.2
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes (see screenshot)
Relevant log outputs (up to 20 lines):
ValueError: Images have shape mismatch: /u/project/silvers/data/bids/IR_bids_pipeline/bids_data/sub-IRA053/fmap/sub-IRA053_magnitude1.nii.gz (96, 96, 3), /u/project/silvers/data/bids/IR_bids_pipeline/bids_data/sub-IRA053/fmap/sub-IRA053_phasediff.nii.gz (96, 96, 72)
