add monai-based scripts for dataset conversion, training, and inference

monai/README.md

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+## Instructions for running inference with the contrast-agnostic spinal cord segmentation model
+
+The following steps are required for using the contrast-agnostic model. 
+
+### Setting up the environment and Installing dependencies
+
+The following commands show how to set up the environment. Note that the documentation assumes that the user has `conda` installed on their system. Instructions on installing `conda` can be found [here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
+
+1. Create a conda environment with the following command:
+
+```bash
+conda create -n venv_monai python=3.9
+```
+
+2. Activate the environment with the following command:
+
+```bash
+conda activate venv_monai
+```
+
+3. The list of necessary packages can be found in `requirements_inference.txt`. Use the following command for installation:
+
+```bash
+pip install -r requirements_inference.txt
+```
+
+### Method 1: Running inference on a single image
+
+The script for running inference is `run_inference_single_image.py`. Please run 
+```
+python run_inference_single_image.py -h
+```
+to get the list of arguments and their descriptions.
+
+
+### Method 2: Running inference on a dataset (Advanced)
+
+NOTE: This section is experimental and for advanced users only. Please use Method 1 for running inference.
+
+#### Creating a datalist
+
+The inference script assumes the dataset to be in Medical Segmentation Decathlon-style `json` file format containing image-label pairs. The `create_inference_msd_datalist.py` script allows to create one for your dataset. Use the following command to create the datalist:
+
+```bash
+python create_inference_msd_datalist.py --dataset-name spine-generic --path-data <path-to-dataset> --path-out <path-to-output-folder> --contrast-suffix T1w
+```
+
+`--dataset-name` - Corresponds to name of the dataset. The datalist will be saved as `<dname>_dataset.json`
+`--path-data` - Path to the BIDS dataset
+`--path-out` - Path to the output folder. The datalist will be saved under `<path-out>/<dname>_dataset.json`
+`--contrast-suffix` - The suffix of the contrast to be used for pairing images/labels
+
+> **Note**
+> This script is not meant to run off-the-shelf. Placeholders are provided to update the script with the .... TODO
+
+
+#### Running inference
+
+Use the following command:
+
+```bash
+python run_inference.py --path-json <path/to/json> --chkp-path <path/to/checkpoint> --path-out <path/to/output> --model <unet/nnunet> --crop_size <48x160x320> --device <gpu/cpu>
+```
+
+`--path-json` - Path to the datalist created in Step 2
+`--chkp-path` - Path to the model checkpoint. This folder should contain the `best_model_loss.ckpt`
+`--path-out` - Path to the output folder where the predictions will be saved
+`--model` - Model to be used for inference. Currently, only `unet` and `nnunet` are supported
+`--crop_size` - Crop size used for center cropping the image before running inference. Recommended to be set to a multiple of 32
+`--device` - Device to be used for inference. Currently, only `gpu` and `cpu` are supported
+
+
+

monai/create_msd_data.py

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+import os
+import json
+from tqdm import tqdm
+import numpy as np
+import argparse
+import joblib
+from utils import FoldGenerator
+from loguru import logger
+from sklearn.model_selection import train_test_split
+
+# root = "/home/GRAMES.POLYMTL.CA/u114716/datasets/spine-generic_uncropped"
+
+parser = argparse.ArgumentParser(description='Code for creating k-fold splits of the spine-generic dataset.')
+
+parser.add_argument('-pd', '--path-data', required=True, type=str, help='Path to the data set directory')
+parser.add_argument('-pj', '--path-joblib', help='Path to joblib file from ivadomed containing the dataset splits.',
+                    default=None, type=str)
+parser.add_argument('-po', '--path-out', type=str, help='Path to the output directory where dataset json is saved')
+parser.add_argument("--contrast", default="t2w", type=str, help="Contrast to use for training", 
+                    choices=["t1w", "t2w", "t2star", "mton", "mtoff", "dwi", "all"])
+parser.add_argument('--label-type', default='soft', type=str, help="Type of labels to use for training",
+                    choices=['hard', 'soft'])
+parser.add_argument('--seed', default=42, type=int, help="Seed for reproducibility")
+args = parser.parse_args()
+
+
+root = args.path_data
+seed = args.seed
+contrast = args.contrast
+if args.label_type == 'soft':
+    logger.info("Using SOFT LABELS ...")
+    PATH_DERIVATIVES = os.path.join(root, "derivatives", "labels_softseg")
+    SUFFIX = "softseg"
+else:
+    logger.info("Using HARD LABELS ...")
+    PATH_DERIVATIVES = os.path.join(root, "derivatives", "labels")
+    SUFFIX = "seg-manual"
+
+# Get all subjects
+# the participants.tsv file might not be up-to-date, hence rely on the existing folders
+# subjects_df = pd.read_csv(os.path.join(root, 'participants.tsv'), sep='\t')
+# subjects = subjects_df['participant_id'].values.tolist()
+subjects = [subject for subject in os.listdir(root) if subject.startswith('sub-')]
+logger.info(f"Total number of subjects in the root directory: {len(subjects)}")
+
+if args.path_joblib is not None:
+    # load information from the joblib to match train and test subjects
+    # joblib_file = os.path.join(args.path_joblib, 'split_datasets_all_seed=15.joblib')
+    splits = joblib.load(args.path_joblib)
+    # get the subjects from the joblib file
+    train_subjects = sorted(list(set([sub.split('_')[0] for sub in splits['train']])))
+    val_subjects = sorted(list(set([sub.split('_')[0] for sub in splits['valid']])))
+    test_subjects = sorted(list(set([sub.split('_')[0] for sub in splits['test']])))
+
+else:
+    # create one json file with 60-20-20 train-val-test split
+    train_ratio, val_ratio, test_ratio = 0.6, 0.2, 0.2
+    train_subjects, test_subjects = train_test_split(subjects, test_size=test_ratio, random_state=args.seed)
+    # Use the training split to further split into training and validation splits
+    train_subjects, val_subjects = train_test_split(train_subjects, test_size=val_ratio / (train_ratio + val_ratio),
+                                                    random_state=args.seed, )
+    # sort the subjects
+    train_subjects = sorted(train_subjects)
+    val_subjects = sorted(val_subjects)
+    test_subjects = sorted(test_subjects)
+
+logger.info(f"Number of training subjects: {len(train_subjects)}")
+logger.info(f"Number of validation subjects: {len(val_subjects)}")
+logger.info(f"Number of testing subjects: {len(test_subjects)}")
+
+# keys to be defined in the dataset_0.json
+params = {}
+params["description"] = "spine-generic-uncropped"
+params["labels"] = {
+    "0": "background",
+    "1": "soft-sc-seg"
+    }
+params["license"] = "nk"
+params["modality"] = {
+    "0": "MRI"
+    }
+params["name"] = "spine-generic"
+params["numTest"] = len(test_subjects)
+params["numTraining"] = len(train_subjects)
+params["numValidation"] = len(val_subjects)
+params["seed"] = args.seed
+params["reference"] = "University of Zurich"
+params["tensorImageSize"] = "3D"
+
+train_subjects_dict = {"train": train_subjects}
+val_subjects_dict = {"validation": val_subjects}
+test_subjects_dict =  {"test": test_subjects}
+all_subjects_list = [train_subjects_dict, val_subjects_dict, test_subjects_dict]
+
+# # define the contrasts
+# contrasts_list = ['T1w', 'T2w', 'T2star', 'flip-1_mt-on_MTS', 'flip-2_mt-off_MTS', 'dwi']
+
+for subjects_dict in tqdm(all_subjects_list, desc="Iterating through train/val/test splits"):
+
+    for name, subs_list in subjects_dict.items():
+
+        temp_list = []
+        for subject_no, subject in enumerate(subs_list):
+
+            if contrast == "all":
+                temp_data_t1w = {}
+                temp_data_t2w = {}
+                temp_data_t2star = {}
+                temp_data_mton_mts = {}
+                temp_data_mtoff_mts = {}
+                temp_data_dwi = {}
+
+                # t1w
+                temp_data_t1w["image"] = os.path.join(root, subject, 'anat', f"{subject}_T1w.nii.gz")
+                temp_data_t1w["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T1w_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t1w["label"]) and os.path.exists(temp_data_t1w["image"]):
+                    temp_list.append(temp_data_t1w)
+
+                # t2w
+                temp_data_t2w["image"] = os.path.join(root, subject, 'anat', f"{subject}_T2w.nii.gz")
+                temp_data_t2w["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T2w_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t2w["label"]) and os.path.exists(temp_data_t2w["image"]):
+                    temp_list.append(temp_data_t2w)
+
+                # t2star
+                temp_data_t2star["image"] = os.path.join(root, subject, 'anat', f"{subject}_T2star.nii.gz")
+                temp_data_t2star["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T2star_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t2star["label"]) and os.path.exists(temp_data_t2star["image"]):
+                    temp_list.append(temp_data_t2star)
+
+                # mton_mts
+                temp_data_mton_mts["image"] = os.path.join(root, subject, 'anat', f"{subject}_flip-1_mt-on_MTS.nii.gz")
+                temp_data_mton_mts["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_flip-1_mt-on_MTS_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_mton_mts["label"]) and os.path.exists(temp_data_mton_mts["image"]):
+                    temp_list.append(temp_data_mton_mts)
+
+                # t1w_mts
+                temp_data_mtoff_mts["image"] = os.path.join(root, subject, 'anat', f"{subject}_flip-2_mt-off_MTS.nii.gz")
+                temp_data_mtoff_mts["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_flip-2_mt-off_MTS_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_mtoff_mts["label"]) and os.path.exists(temp_data_mtoff_mts["image"]):
+                    temp_list.append(temp_data_mtoff_mts)
+
+                # dwi
+                temp_data_dwi["image"] = os.path.join(root, subject, 'dwi', f"{subject}_rec-average_dwi.nii.gz")
+                temp_data_dwi["label"] = os.path.join(PATH_DERIVATIVES, subject, 'dwi', f"{subject}_rec-average_dwi_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_dwi["label"]) and os.path.exists(temp_data_dwi["image"]):
+                    temp_list.append(temp_data_dwi)
+
+
+            elif contrast == "t1w":     # t1w
+                temp_data_t1w = {}
+                temp_data_t1w["image"] = os.path.join(root, subject, 'anat', f"{subject}_T1w.nii.gz")
+                temp_data_t1w["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T1w_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t1w["label"]) and os.path.exists(temp_data_t1w["image"]):
+                    temp_list.append(temp_data_t1w)
+                else:
+                    logger.info(f"Subject {subject} does not have T1w image or label.")
+
+
+            elif contrast == "t2w":     # t2w
+                temp_data_t2w = {}
+                temp_data_t2w["image"] = os.path.join(root, subject, 'anat', f"{subject}_T2w.nii.gz")
+                temp_data_t2w["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T2w_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t2w["label"]) and os.path.exists(temp_data_t2w["image"]):
+                    temp_list.append(temp_data_t2w)
+                else:
+                    logger.info(f"Subject {subject} does not have T2w image or label.")
+
+
+            elif contrast == "t2star":     # t2star
+                temp_data_t2star = {}
+                temp_data_t2star["image"] = os.path.join(root, subject, 'anat', f"{subject}_T2star.nii.gz")
+                temp_data_t2star["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_T2star_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_t2star["label"]) and os.path.exists(temp_data_t2star["image"]):
+                    temp_list.append(temp_data_t2star)
+                else:
+                    logger.info(f"Subject {subject} does not have T2star image or label.")
+
+
+            elif contrast == "mton":     # mton_mts
+                temp_data_mton_mts = {}
+                temp_data_mton_mts["image"] = os.path.join(root, subject, 'anat', f"{subject}_flip-1_mt-on_MTS.nii.gz")
+                temp_data_mton_mts["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_flip-1_mt-on_MTS_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_mton_mts["label"]) and os.path.exists(temp_data_mton_mts["image"]):
+                    temp_list.append(temp_data_mton_mts)
+                else:
+                    logger.info(f"Subject {subject} does not have MTOn image or label.")
+
+            elif contrast == "mtoff":     # t1w_mts
+                temp_data_mtoff_mts = {}
+                temp_data_mtoff_mts["image"] = os.path.join(root, subject, 'anat', f"{subject}_flip-2_mt-off_MTS.nii.gz")
+                temp_data_mtoff_mts["label"] = os.path.join(PATH_DERIVATIVES, subject, 'anat', f"{subject}_flip-2_mt-off_MTS_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_mtoff_mts["label"]) and os.path.exists(temp_data_mtoff_mts["image"]):
+                    temp_list.append(temp_data_mtoff_mts)
+                else:
+                    logger.info(f"Subject {subject} does not have MTOff image or label.")
+
+            elif contrast == "dwi":     # dwi
+                temp_data_dwi = {}
+                temp_data_dwi["image"] = os.path.join(root, subject, 'dwi', f"{subject}_rec-average_dwi.nii.gz")
+                temp_data_dwi["label"] = os.path.join(PATH_DERIVATIVES, subject, 'dwi', f"{subject}_rec-average_dwi_{SUFFIX}.nii.gz")
+                if os.path.exists(temp_data_dwi["label"]) and os.path.exists(temp_data_dwi["image"]):
+                    temp_list.append(temp_data_dwi)
+                else:
+                    logger.info(f"Subject {subject} does not have DWI image or label.")
+
+            else:
+                raise ValueError(f"Contrast {contrast} not recognized.")
+
+
+        params[name] = temp_list
+        logger.info(f"Number of images in {name} set: {len(temp_list)}")
+
+final_json = json.dumps(params, indent=4, sort_keys=True)
+if not os.path.exists(args.path_out):
+    os.makedirs(args.path_out, exist_ok=True)
+
+jsonFile = open(args.path_out + "/" + f"dataset_{contrast}_{args.label_type}_seed{seed}.json", "w")
+jsonFile.write(final_json)
+jsonFile.close()
+
+
+
+
+
+