SLURM workflow for building a 25 µm rat brain template with modelbuild.sh (ANTs, QBatch).

• rat_build_template_25um.sh — Build driver: parses args, cds into the template working dir, checks list files, runs modelbuild.sh (rigid → similarity → affine → nlin) with 10‑day walltimes. Logs to a timestamped file in the working dir.
• slurm_wrapper_rat_template_25um.sh — SLURM wrapper: loads the template-builder module, sets QBatch env vars, then runs the build script. Does not run registrations itself; it submits the jobs and exits.

• Atlas-forge root: <atlas_dir> (e.g. ATLAS_DIR/SPECIES).
• Templates: <atlas_dir>/templates/<template_name>.
• Each template dir must contain:
  • brain_paths_flipped_res-25um.txt
  • mask_paths_flipped_res-25um.txt
  • modelbuild.sh (from your atlas-forge/template-builder setup).

1. Deploy scripts
   Copy or symlink both scripts to the same location (or where the wrapper can find the build script). The wrapper’s default BUILD_SCRIPT is <atlas_dir>/<species>/scripts/rat_build_template_25um.sh. If you put them elsewhere, override at submit time:
   sbatch --export=ALL,BUILD_SCRIPT=/path/to/rat_build_template_25um.sh slurm_wrapper_rat_template_25um.sh

2. Submit the wrapper (from the directory that contains the wrapper, or use an absolute path):

   sbatch slurm_wrapper_rat_template_25um.sh

3. Override defaults (optional):

   sbatch --export=ALL,ATLAS_DIR=/path,SPECIES=rat_atlas,TEMP_NAME=swc_female_rat_template_res-25um_n-15,AVE_TYPE=efficient_trimean slurm_wrapper_rat_template_25um.sh

• SLURM, QBatch, and a template-builder module (or equivalent) providing modelbuild.sh and ANTs. Module path and defaults in the wrapper are site-specific (e.g. UCL Neuroinformatics).