Fmriprep: error: Path does not exist

1

Hi,

I am running the new version of fmriprep: 20.2.1. But it returned:
fmriprep: error: Path does not exist: </mnt/data1/data/wsj/bids/>.

My command:
singularity run --cleanenv ~/Documents/simgs/fmriprep-20.2.1.simg /mnt/data1/data/wsj/bids/ --output-layout bids participant --fs-license-file ~/Documents/license.txt -output-spaces MNI152NLin6Asym T1w -w /mnt/data1/data/wsj/work/ --participant-label 01

And I am sure that path exists.

(My system is installed on SSD, while the data is on another HDD. Not sure if it is related.)

Could you please help me to see what is wrong?

Thanks,
Best,
Liwei

2

Hi Liwei,

When you run Singularity, you’ll want to bind the drive where the data lives to the singularity container. You do that by adding -B /mnt to the singularity command (you can do it right after --cleanenv). Also, you may need to do the same thing with your ~ drive, so singularity can find the license file. Does this make sense?

Best,
Steven

3

Thank you very much, Steven. It works great. I think ~ drive ($HOME) is already included in the system defined bind points. See: Bind Paths | Singularity

1 Like
4

Great! Yah I presumed ~ may have been added by default, but better safe than sorry. Happy it worked out!