Apptainer containers¶

Lab wrapper (this cluster)¶

cd /path/to/dlsurfer
source env/cluster_containers.sh

Sets:

Variable	Meaning
`FASTSURFER_HOME`	Wrapper dir with `run_fastsurfer.sh` → SIF
`FREESURFER_HOME`	Thin FS home + `env/bin/*` tool wrappers
`FS_LICENSE`	FreeSurfer license path
`DLSURFER_SIF_` / `SIF_`	Paths to FastSurfer, LIT, FreeSurfer SIFs

Wrappers under env/bin/ (lit-inpainting, mri_synthstrip, mris_estimate_wm, …) call apptainer exec with NFS binds. GPU tools pass --nv when nvidia-smi is available (DLSURFER_FASTSURFER_NV, DLSURFER_LIT_NV, DLSURFER_FS_NV).

Expected SIF names (example)¶

fastsurfer_cu126_v2.6.0.sif
lit_0.6.0.sif
freesurfer_7.4.1.sif

Point env/cluster_containers.sh (or env vars) at your container store. Do not commit SIFs or license files to git.

Optional meta-image¶

containers/dlsurfer.def is a scaffold for a single image that bundles the CLI; production runs here use the three SIFs above.