| # SimCortex segmentation inference config | |
| dataset: | |
| # Single-dataset mode: | |
| # set path to one preprocessed derivative root and keep roots null/empty. | |
| # Multi-dataset mode: | |
| # keep path null and define roots below. | |
| path: null | |
| split_file: /path/to/datasets/splits/dataset_split.csv | |
| # Use "all" to create inputs for downstream InitSurf and deformation stages. | |
| # Use "test" only for a test-only inference run. | |
| split_name: all | |
| session_label: "01" | |
| space: "MNI152" | |
| pad_mult: 16 | |
| roots: | |
| HCP_YA: /path/to/datasets/hcpya-u100/derivatives/sc-preproc | |
| OASIS1: /path/to/datasets/oasis-1/derivatives/sc-preproc | |
| model: | |
| in_channels: 1 | |
| out_channels: 9 | |
| features: [16, 32, 64, 128, 128] | |
| norm: instance | |
| dropout: 0.10 | |
| ckpt_path: /path/to/seg_best_dice.pt | |
| trainer: | |
| device: cuda:0 | |
| batch_size: 1 | |
| num_workers: 2 | |
| amp: true | |
| outputs: | |
| # Single-dataset mode: | |
| out_root: null | |
| # Multi-dataset mode: | |
| out_roots: | |
| HCP_YA: /path/to/datasets/hcpya-u100/derivatives/sc-seg | |
| OASIS1: /path/to/datasets/oasis-1/derivatives/sc-seg | |
| log_dir: /path/to/simcortex-runs/seg/logs_infer | |
| overwrite: false | |
| overwrite_dataset_description: false | |
| tensorboard: true | |
| hydra: | |
| run: | |
| dir: ${outputs.log_dir} | |
| output_subdir: null | |
| job: | |
| chdir: false |