update prepare datalist function

configs/inference.json

@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "/workspace/brats_mri_segmentation",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/configs/datalist.json'",

configs/metadata.json

@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.4",
+    "version": "0.3.5",
     "changelog": {
+        "0.3.5": "update prepare datalist function",
         "0.3.4": "update output format of inference",
         "0.3.3": "update to use monai 1.0.1",
         "0.3.2": "enhance readme on commands example",

configs/train.json

@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "/workspace/brats_mri_segmentation",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/configs/datalist.json'",

scripts/prepare_datalist.py

@@ -47,7 +47,7 @@ def main(args):
     """
     split the dataset and output the data list into a json file.
     """
-    data_file_base_dir = os.path.join(args.path, "training")
+    data_file_base_dir = os.path.join(os.path.abspath(args.path), "training")
     output_json = args.output
     # produce deterministic data splits
     monai.utils.set_determinism(seed=123)