Summary of what happened:
fmriprep fails on Freesurfer auto-recon step. I have used the same Singularity containers in the past without issue, and the error message (from FreeSurfer, that a subject number hasn’t been specified) doesn’t make sense because the output includes a subject number in the command that fmriprep passed to Freesurfer.
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/sh
#SBATCH --partition=caslake
#SBATCH --time=36:00:00
#SBATCH -N 1
#SBATCH -c 8
#SBATCH --mem-per-cpu=16000
#SBATCH -J fmriprep_BF_042
#SBATCH --account=pi-decety
#SBATCH --output=fmriprep_BF_042-srun++.out
#SBATCH --error=fmriprep_BF_042-srun++.err
echo "SLURM_JOBID="$SLURM_JOBID
echo "SLURM_JOB_NODELIST"=$SLURM_JOB_NODELIST
echo "SLURM_NNODES"=$SLURM_NNODES
echo "SLURMTMPDIR="$SLURMTMPDIR
echo "working directory = "$SLURM_SUBMIT_DIR
module load intel/13.1
module load intel-mpi/4.1.3
module load singularity
module unload fsl
module list
ulimit -s unlimited
export TEMPLATEFLOW_HOME=/project/decety/templateflow
export SINGULARITYENV_TEMPLATEFLOW_HOME=/project/decety/templateflow
NPROCS=`srun --nodes=${SLURM_NNODES} bash -c 'hostname' |wc -l`
echo NPROCS=$NPROCS
echo "Launch fmriprep with srun"
#The PMI library is necessary for srun
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
srun singularity run -B /project/decety -B /scratch/midway3/mscohen /project/decety/my_images/fmriprep-23.1.4.simg --participant_label=042 --fs-license-file="/project/decety/freesurfer_license.txt" -v -v --nthreads 4 --output-spaces MNI152NLin6Asym:res-2 --bold2t1w-dof 6 --use-aroma --fd-spike-threshold 0.9 --dvars-spike-threshold 3 --skull-strip-template OASIS30ANTs -w /scratch/midway3/mscohen /project/decety/BrainFog_BIDS /project/decety/BrainFog_BIDS/derivatives/fmriprep participant
Version:
23.1.4 and 22.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity container
Data formatted according to a validatable standard? Please provide the output of the validator:
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)
Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
483 Files, 5.9GB estroop MRI
17 - Subjects flanker
2 - Sessions rest
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
Cmdline:
recon-all -autorecon1 -i /scratch/midway3/mscohen/fmriprep_23_1_wf/single_subject_042_wf/anat_preproc_wf/anat_template_wf/anat_merge/sub-042_ses-01_T1w_noise_corrected_template.nii.gz -noskullstrip -noT2pial -noFLAIRpial -hires -openmp 3 -subjid sub-042 -sd /project/decety/BrainFog_BIDS/derivatives/fmriprep/sourcedata/freesurfer -expert /scratch/midway3/mscohen/fmriprep_23_1_wf/single_subject_042_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
Stdout:
ERROR: must specify a subject id
Stderr:
mktemp: failed to create file via template ‘/scratch/local/jobs/19320194/tmp.XXXXXXXXXX’: No such file or directory
mktemp: failed to create file via template ‘/scratch/local/jobs/19320194/tmp.XXXXXXXXXX’: No such file or directory
Traceback (most recent call last):
File "/opt/freesurfer/python/scripts/rca-config2csh", line 20, in <module>
configfile = sys.argv[1]
IndexError: list index out of range
Traceback:
RuntimeError: subprocess exited with code 1.