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cd89698 69bd6d1 cd89698 6727502 cd89698 6727502 cd89698 69bd6d1 cd89698 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 | # Configuration
YAML values always override CLI defaults (`args.__dict__.update(config)`). To override a YAML value, edit the YAML file or omit the key so the CLI default is used.
```bash
python run_pirads.py --mode train --config config/config_pirads_train.yaml
```
## PI-RADS Training Parameters
| Parameter | Default | Description |
|-----------|---------|-------------|
| `mode` | — | `train` or `test` (required) |
| `config` | — | Path to YAML config file |
| `data_root` | — | Root folder of T2W images |
| `dataset_json` | — | Path to dataset JSON file. Format should be as specified in [Getting Started](getting-started.md) |
| `num_classes` | `4` | Number of output classes (PI-RADS 2–5) |
| `mil_mode` | `att_trans` | MIL algorithm (`mean`, `max`, `att`, `att_trans`, `att_trans_pyramid`) |
| `tile_count` | `24` | Number of patches per scan |
| `tile_size` | `64` | Patch spatial size in pixels |
| `depth` | `3` | Number of slices per patch |
| `use_heatmap` | `True` | Enable heatmap-guided patch sampling |
| `workers` | `2` | DataLoader workers |
| `checkpoint` | `None` | Path to resume from checkpoint |
| `epochs` | `50` | Max training epochs |
| `early_stop` | `40` | Epochs without improvement before stopping |
| `batch_size` | `4` | Scans per batch |
| `optim_lr` | `3e-5` | Base learning rate |
| `weight_decay` | `0` | Optimizer weight decay |
| `amp` | `False` | Enable automatic mixed precision |
| `val_every` | `1` | Validation frequency (epochs) |
| `wandb` | `False` | Enable Weights & Biases logging |
| `project_name` | `Classification_prostate` | W&B project name |
| `run_name` | `train_pirads` | Run name for logging. If using SLURM, takes SLURM JOB_ID |
## csPCa Training Parameters
| Parameter | Default | Description |
|-----------|---------|-------------|
| `mode` | — | `train` or `test` (required) |
| `config` | — | Path to YAML config file |
| `data_root` | — | Root folder of images |
| `dataset_json` | — | Path to dataset JSON file |
| `checkpoint_pirads` | — | Path to pre-trained PI-RADS model (required for train) |
| `checkpoint_cspca` | — | Path to csPCa checkpoint (required for test) |
| `epochs` | `30` | Max training epochs |
| `batch_size` | `32` | Scans per batch |
| `optim_lr` | `2e-4` | Learning rate |
| `num_seeds` | `20` | Number of random seeds for CI |
Shared parameters (`num_classes`, `mil_mode`, `tile_count`, `tile_size`, `depth`, `use_heatmap`, `workers`, `val_every`) have the same defaults as PI-RADS.
## Preprocessing Parameters
| Parameter | Default | Description |
|-----------|---------|-------------|
| `config` | — | Path to YAML config file |
| `steps` | — | Steps to execute (required, one or more) |
| `t2_dir` | — | Directory of T2W images |
| `dwi_dir` | — | Directory of DWI images |
| `adc_dir` | — | Directory of ADC images |
| `seg_dir` | — | Directory of segmentation masks |
| `output_dir` | — | Output directory |
| `margin` | `0.2` | Center-crop margin fraction |
## Example YAML
=== "PI-RADS Training"
```yaml
data_root: /path/to/registered/t2_hist_matched
dataset_json: /path/to/PI-RADS_data.json
num_classes: 4
mil_mode: att_trans
tile_count: 24
tile_size: 64
depth: 3
use_heatmap: true
workers: 4
epochs: 100
batch_size: 8
optim_lr: 2e-4
weight_decay: 1e-5
amp: true
wandb: true
```
=== "csPCa Training"
```yaml
data_root: /path/to/registered/t2_hist_matched
dataset_json: /path/to/csPCa_data.json
num_classes: 4
mil_mode: att_trans
tile_count: 24
tile_size: 64
depth: 3
use_heatmap: true
workers: 6
checkpoint_pirads: /path/to/models/pirads.pt
epochs: 80
batch_size: 8
optim_lr: 2e-4
```
=== "Preprocessing"
```yaml
t2_dir: /path/to/raw/t2
dwi_dir: /path/to/raw/dwi
adc_dir: /path/to/raw/adc
output_dir: /path/to/processed
```
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