fMRIPrep 25.1.1 recon-all error: “no run data found in …/freesurfer/sub-XXX/mri”

Software Support
1

Hi all

Summary of what happened:

I’m encountering an error when running fMRIPrep version 25.1.1 that wasn’t present in 25.0.0. The preprocessing pipeline stops during the first recon-all Freesurfer step.

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

setenv SUBJECTS_DIR /scratch/… /freesurfer

/opt/freesurfer/bin/recon-all -autorecon1 -i /work/fmriprep_25_1_wf/sub_149_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-149_ses-01_T1w_noise_corrected.nii.gz -T2 /scratch/… /sub-149/ses-01/anat/sub-149_ses-01_acq-norm_T2w.nii.gz -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-149 -sd /scratch/…/freesurfer

Version:

fMRIPrep version 25.1.1

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

Singularity

Relevant log outputs (up to 20 lines):

ERROR: no run data found in /scratch/.../freesurfer/sub-149/mri. Make sure to have a volume called 001.mgz in scratch/.../freesurfer/sub-149/mri/orig. If you have a second run of data call it 002.mgz, etc.

Earlier in the log, mri_convert appears to run successfully and valid 001.mgz and T2raw.mgz files can be found in the specified locations:

writing to /scratch/… /freesurfer/sub-149/mri/orig/001.mgz... 

writing to /scratch/…/ freesurfer/sub-149/mri/orig/T2raw.mgz...

Screenshots / relevant information:

This same dataset runs fine in fMRIPrep 25.0.0, and the 001.mgz file is found without issues.

Has anyone experienced something similar with fMRIPrep 25.1.1? Any suggestions on how to resolve this would be greatly appreciated!

Many thanks
Anja

2

Hi @Anja,

Please provide your fmriprep command.

Best,
Steven

3

Hi Steven

This is my fMRIPrep command:

SINGULARITY_CMD="singularity run --cleanenv \
-B $BIDS_DIR:/data \
-B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} \
-B $WORK_DIR:/work \
 $FMRIPREP"

cmd="${SINGULARITY_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant \
--participant-label $subject -w /work -vv --nthreads $SLURM_CPUS_PER_TASK \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym \
--skip_bids_validation \
--fs-license-file $SURF_LICENSE \
--use-syn-sdc"

Many thanks
Anja