Fmriprep error: mount source /lustre doesn't exist

ttan · September 14, 2021, 1:32am

Hello,

I’m trying to run fmriprep on a cluster via singularity. However, I received the following error messages:

WARNING: skipping mount of /lustre: stat /lustre: no such file or directory
FATAL: container creation failed: mount /lustre->/lustre error: while mounting /lustre: mount source /lustre doesn’t exist

Here’s the command line I used:

singularity run --cleanenv /home/hon9005/fmriprep-20.2.3.simg
/data /data/derivatives
participant
–participant-label sub-093264

I’d really appreciate help or insight into how to get fmriprep running. Thank you very much.

Steven · September 14, 2021, 2:21pm

A few things:

You should bind all relevant drives to singularity, so between singularity run and --cleanenv add something like -B /data or -B /lustre (or both, depends on your HPC organization)
You’ll need to specify a path to a valid Freesurfer license with the --fs-license-file argument.
Might just be how it’s copied and pasted here, but if arguments are on different lines, they should be separated by a \ at the end of each line so your terminal knows that they are part of the same command.

Hope this helps,
Steven