Fmriprep fails to run Freesurfer auto-recon

Software Support
,
1

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.

Screenshots / relevant information:

2

Hi @michaelcohen,

Does the error persist when adding -e to the singularity preamble which makes sure nothing from your computational environment is carried into the container?

Best,
Steven

3

Oh it looks like that was the problem! Good catch. It looks like it runs successfully when I include that flag. (I had used the --cleanenv flag in other scripts, which I assume does the same thing?, but had accidentally left it out here.)

Thanks,
Michael

4