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AMOS22 CT->MRI shared-13 SACFlow-FM runbook

This protocol uses AMOS CT as source and AMOS MRI as target. Labels 14 and 15 are mapped to background because the MRI validation split may not contain them. The resulting task has 14 classes: background 0 and foreground labels 1..13.

0. Build manifests 

AMOS_ROOT=datasets/amos22 bash scripts/amos/00_make_manifests.sh

This creates:

  • data_json/amos_ct2mr.json: original CT/MRI split.
  • data_json/amos_ct2mr_shared13.json: labels 14/15 remapped to background, target labels retained.
  • data_json/amos_ct2mr_shared13_sfda.json: same remapping, but target-train labels removed.

1. Smoke test 

NPROC=1 bash scripts/amos/01_smoke_source_ct.sh

2. Main sanity ladder 

NPROC=8 bash scripts/amos/train_source_ct.sh
bash scripts/amos/eval_source_ct2mri.sh
bash scripts/amos/export_memory_ct.sh
NPROC=8 bash scripts/amos/train_oracle_mri.sh
NPROC=8 bash scripts/amos/run_selftrain_ct2mri.sh
NPROC=8 bash scripts/amos/run_peft_ct2mri.sh
NPROC=8 bash scripts/amos/run_proto_align_ct2mri.sh
NPROC=8 bash scripts/amos/run_sacflow_ct2mri.sh
bash scripts/amos/eval_all_main.sh

3. SACFlow ablations 

NPROC=8 bash scripts/amos/run_sacflow_linear_ct2mri.sh
NPROC=8 bash scripts/amos/run_sacflow_whole_feature_ct2mri.sh
NPROC=8 bash scripts/amos/run_sacflow_random_subspace_ct2mri.sh

Notes

  • Evaluate on target_val, because target_test in the downloaded AMOS22 release may not include labels.
  • Use data_json/amos_ct2mr_shared13_sfda.json for SFDA/adaptation runs to avoid target-label leakage.
  • Use data_json/amos_ct2mr_shared13.json only for oracle training or debug.
  • The first table should include source-only, target oracle, self-training, PEFT-only, proto-align, and SACFlow-FM.