Add files using upload-large-folder tool

brain-structure.py

@@ -133,47 +133,50 @@ class BrainStructure(datasets.GeneratorBasedBuilder):
         id_ = 0
         for root, dirs, files in os.walk(data_dir):
             for fname in files:
-                if fname.endswith("_scandata.json"):
-                    sidecar_path = os.path.join(root, fname)
-                    with open(sidecar_path, "r") as f:
-                        sidecar = json.load(f)
-
-                    # Only yield if 'split' matches the requested split
-                    if sidecar.get("split") == desired_split:
-                        # Locate corresponding NIfTI .nii.gz
-                        nii_prefix = fname.replace("_scandata.json", "_T1w")
-                        nii_filepath = None
-                        for potential_file in files:
-                            if (potential_file.startswith(nii_prefix) 
-                                and potential_file.endswith(".nii.gz")):
-                                nii_filepath = os.path.join(root, potential_file)
-                                break
-
-                        if not nii_filepath:
-                            logger.warning(f"No .nii.gz found for {sidecar_path}")
-                            continue
-
-                        yield id_, {
-                            "id": str(id_),
-                            "nii_filepath": nii_filepath,
-                            "metadata": {
-                                "split": sidecar.get("split", ""),
-                                "participant_id": sidecar.get("participant_id", ""),
-                                "session_id": sidecar.get("session_id", ""),
-                                "study": sidecar.get("study", ""),
-                                "age": sidecar.get("age", 0),
-                                "sex": sidecar.get("sex", ""),
-                                "clinical_diagnosis": sidecar.get("clinical_diagnosis", ""),
-                                "scanner_manufacturer": sidecar.get("scanner_manufacturer", ""),
-                                "scanner_model": sidecar.get("scanner_model", ""),
-                                "field_strength": sidecar.get("field_strength", ""),
-                                "image_quality_rating": float(sidecar.get("image_quality_rating", 0.0)),
-                                "total_intracranial_volume": float(sidecar.get("total_intracranial_volume", 0.0)),
-                                "license": sidecar.get("license", ""),
-                                "website": sidecar.get("website", ""),
-                                "citation": sidecar.get("citation", ""),
-                                "t1_file_name": sidecar.get("t1_file_name", ""),
-                                "radiata_id": sidecar.get("radiata_id", 0),
-                            },
-                        }
-                        id_ += 1
+                # Only consider sidecar files that start with "msub" and end with "_scandata.json"
+                if not (fname.startswith("msub") and fname.endswith("_scandata.json")):
+                    continue
+
+                sidecar_path = os.path.join(root, fname)
+                with open(sidecar_path, "r") as f:
+                    sidecar = json.load(f)
+
+                # if sidecar's "split" matches the desired_split...
+                if sidecar.get("split") == desired_split:
+                    # attempt to find the .nii.gz with the same "msub" prefix
+                    possible_nii_prefix = fname.replace("_scandata.json", "_T1w")
+                    nii_filepath = None
+                    for potential_file in files:
+                        if (potential_file.startswith(possible_nii_prefix) 
+                            and potential_file.endswith(".nii.gz")):
+                            nii_filepath = os.path.join(root, potential_file)
+                            break
+
+                    if not nii_filepath:
+                        logger.warning(f"No corresponding .nii.gz file found for {sidecar_path}")
+                        continue
+
+                    yield id_, {
+                        "id": str(id_),
+                        "nii_filepath": nii_filepath,
+                        "metadata": {
+                            "split": sidecar.get("split", ""),
+                            "participant_id": sidecar.get("participant_id", ""),
+                            "session_id": sidecar.get("session_id", ""),
+                            "study": sidecar.get("study", ""),
+                            "age": sidecar.get("age", 0),
+                            "sex": sidecar.get("sex", ""),
+                            "clinical_diagnosis": sidecar.get("clinical_diagnosis", ""),
+                            "scanner_manufacturer": sidecar.get("scanner_manufacturer", ""),
+                            "scanner_model": sidecar.get("scanner_model", ""),
+                            "field_strength": sidecar.get("field_strength", ""),
+                            "image_quality_rating": float(sidecar.get("image_quality_rating", 0.0)),
+                            "total_intracranial_volume": float(sidecar.get("total_intracranial_volume", 0.0)),
+                            "license": sidecar.get("license", ""),
+                            "website": sidecar.get("website", ""),
+                            "citation": sidecar.get("citation", ""),
+                            "t1_file_name": sidecar.get("t1_file_name", ""),
+                            "radiata_id": sidecar.get("radiata_id", 0),
+                        },
+                    }
+                    id_ += 1