Reposting from https://github.com/poldracklab/fmriprep/issues/1687
The problem is that fMRIPrep (with Singularity) fails because TemplateFlow is trying to pull down a new template but the TemplateFlow home folder is read-only.
This problem has been addressed for fMRIPrep version 1.4.1rc4 or later. If your Singularity installation automatically binds your home directory, it should work out of the box.
Otherwise, you’ll need to bind some writable folder for templateflow (e.g.,
$HOME/.templateflow) after having exported a new templateflow home:
export SINGULARITYENV_TEMPLATEFLOW_HOME=/opt/templateflow singularity run -B $HOME/.templateflow:/opt/tempalteflow ...