fsl6 Docker Image

Software Included
Dockerfile
Run on LSF

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
```
ghcr.io/washu-it-ris/fsl:latest
```
Code repository is on GitHub and requires access to be granted by an administrator.

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

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(ghcr.io/washu-it-ris/fsl:latest)' /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(ghcr.io/washu-it-ris/fsl:latest)' /bin/bash

Non-Interactive

bsub -a 'docker(ghcr.io/washu-it-ris/fsl:latest)' {command & arguments to run}