Singularity instead of docker with the dHCP

1

Our lab uses singularity to “pull” docker when running the dHCP. This requires us to use . /etc/fsl/fsl.sh. Docker allows an -e option that condenses the two steps of setting the shell up for FSL and running the pipeline. Was wondering if there was a similar command for singularity? Thanks!

2

Hello @cpletcher,

I’m sorry, I don’t know. I think I would try asking on the singularity forums.

3

Hi, can you give a bit more detail of the docker image you pulled and how you tried to run? I used singularity to run dhcp pipeline with tag “emma” successfully.

Best regards,
Jianliang

4

Hello! What we did is use ./etc/fsl/fsl.sh first. The image we pulled was from our subject data, we set up singularity and then used singularity run -B $PWD/data:/data dhcp-structural-pipeline_latest subject1 session1 44-T1 data/T1w.nii.gz -T2 data/T2w.nii.gz -t num.