fsl6 Docker Image
- RIS-SVC-conf-publish
- Brennan Mulligan
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}