Poor segmentation observed in fmri pre html

Summary of what happened:

Despite observed correct segmentation from freesurfer recon, during QC of the fmriprept HTML report we found large portions of what and gray matter were not segmented for a handful of particpants. recon was ran before running fmri prep.

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

singularity_cmd = f"singularity run \
    --cleanenv \
    /home/data/madlab/singularity-images/nipreps_fmriprep_20.2.3.sif \
    {output_dir}/fmriprep_dset/ \
    {output_dir}/fmriprep_derivatives/ participant \
    -w /scratch/madlab/fmriprep/emuR01_work \
    --participant_label {' '.join(subjects)} \
    --skull-strip-template MNIPediatricAsym:cohort-5 \
    --output-spaces MNIPediatricAsym:cohort-5:res-2 \
    --fs-license-file=/scratch/madlab/license.txt \
    --skip-bids-validation \
    --bids-database-dir {output_dir}/bids_layout \
    --clean-workdir \
    --nthreads 40 \
    --omp-nthreads 40"



Environment (Docker, Singularity, custom installation):

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

BIDS standard

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

From fmriprep: