fsl6 Docker Image

Compute Resources

• Have questions or need help with compute, including activation or issues? Follow this link.

• User Agreement

Docker Usage

• The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.

• Docker and the RIS Compute Service

• Docker Basics: Building, Tagging, & Pushing A Custom Docker Image

Software Included

• Functional MRI: FEAT, MELODIC, FABBER, BASIL, VERBENA

• Structural MRI: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat

• Diffusion MRI: FDT, TBSS, XTRACT, eddy, topup, eddyqc

• GLM /Stats: GLM general advice, Randomise, PALM, Cluster, FDR, Dual Regression, Mm, FLOBS

• Other: FSLeyes, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST

Dockerfile

Versions

• Docker image hosted at

  gcr.io/ris-registry-shared/fsl6
  

• Minimum Docker image hosted at

  gcr.io/ris-registry-shared/fsl6_min
  

• Code repository is located at BitBucket and requires Wustl VPN connection and a wustlkey to access.

Run on LSF

Preserve Environment variables

• Paths inside the container are not being preserved unless one sets this variable for the whole session.

  • export LSF_DOCKER_PRESERVE_ENVIRONMENT=false

  • Prepend LSF_DOCKER_PRESERVE_ENVIRONMENT=false before an individual bsub command (in which case the variable is only false for that command).

• If one fails to set preserve environment variable to false, one would have to provide each application’s full path.

bsub Command

Note

If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.

• Interactive Session

  bsub -Is -q general-interactive -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' /bin/bash
  

• Alternatively, if you want the preserve environment to only be false for one command.

  LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -Is -q general-interactive -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' /bin/bash
  

• Non-Interactive

  bsub -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' {command & arguments to run}