Medical Spine Sagittal MRI Dataset for Segmentation and Foraminal Stenosis detection.
The 7 matches
- [1] § Data Records ↔ models/position_of_slices.ipynb, lines 334–420 · score 0.90 · L3 L4, L4 L5, L2 L3, AISSLab, patient ID, L5 S1
- [2] § Technical Validation › Preprocessing ↔ models/Custom_CNN.ipynb, lines 37–73 · score 0.80 · Gaussian blur, vertical flips, noise, brightness, horizontal, gamma
- [3] § Technical Validation › Sagittal MRI foraminal stenosis detection ↔ models/Custom_CNN.ipynb, lines 121–196 · score 0.69 · weight decay, dropout rate, layers, CNN, optimized, module
- [4] § Methodology › Data curation ↔ de_identification.py, lines 7–23 · score 0.64 · patient history, de identification, ethnic, physician
- [5] § Technical Validation › Sagittal MRI foraminal stenosis detection ↔ models/Diet_model.ipynb, lines 156–298 · score 0.61 · mAP, dropout, recall, scores, architecture, DeiT
- [6] § Methodology › Sagittal foraminal detection and classification ↔ models/position_of_slices.ipynb, lines 334–420 · score 0.61 · L5 S1, L1 L2, xmax, xmin, ymax, ymin
- [7] § Technical Validation › Sagittal MRI segmentation ↔ models/Diet_model.ipynb, lines 156–298 · score 0.58 · Windows, configuration, metrics, Recall, CPU, architectures
Paper
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The authors' code
Jupyter notebook · 509 lines · 16 KB · no license · 2 matches
- # %% [markdown]
- # #### builld the dataset
- # %%
- import os
- import pydicom
- def detect_scan_direction(folder):
- slices = []
- for f in sorted(os.listdir(folder)):
- path = os.path.join(folder, f)
- ds = pydicom.dcmread(path)
- if "ImagePositionPatient" not in ds:
- continue
- x = ds.ImagePositionPatient[0] # X coordinate
- slices.append((f, x))
- if len(slices) < 2:
- print("Not enough slices to determine direction.")
- return
- first_x = slices[0][1]
- last_x = slices[-1][1]
- if first_x < last_x:
- print("Scan direction: Right → Left")
- else:
- print("Scan direction: Left → Right")
- for name, x in slices:
- print(f"{name}: X = {x:.2f}")
- # Example usage
- # detect_scan_direction(r"Sagittal")
- # detect_scan_direction(r"D:\Dataset\DatasetV0.17 Dicom format - Correct version\PATIENT672717\ST000000-MR, VERTEBRA, LOMBER\SE000000-Sag T2 frFSE"
- # detect_scan_direction(r"D:\AISSLab\Code\3D CNN\datasets\DatasetV0.17 Dicom format - Correct version\PATIENT62951\ST000000-MR, LOMBER\SE000000-Sag T2 frFSE")
- # detect_scan_direction(r"D:\AISSLab\Code\3D CNN\datasets\DatasetV0.17 Dicom format - Correct version\PATIENT110343\ST000000-MRG, LOMBER VERTEBRA, KONTRASTSIZ\SE000000-T2W_TSE")
- # opisite
- # %%
- import os
- root_folder = r"D:\Dataset\DatasetV0.17 Dicom format - Correct version"
- for patient_name in os.listdir(root_folder):
- patient_folder = os.path.join(root_folder, patient_name)
- if not os.path.isdir(patient_folder):
- continue
- folder_file_counts = {}
- for item in os.listdir(patient_folder):
- item_path = os.path.join(patient_folder, item)
- if os.path.isdir(item_path):
- for scan_module in os.listdir(item_path):
- scan_path = os.path.join(item_path, scan_module)
- if os.path.isdir(scan_path):
- file_count = sum(len(files) for _, _, files in os.walk(scan_path))
- folder_file_counts[scan_path] = file_count
- if folder_file_counts:
- # Identify the longest and shortest folders
- longest_folder = max(folder_file_counts, key=folder_file_counts.get)
- shortest_folder = min(folder_file_counts, key=folder_file_counts.get)
- # Define new paths
- axial_path = os.path.join(os.path.dirname(longest_folder), "Axial")
- sagittal_path = os.path.join(os.path.dirname(shortest_folder), "Sagittal")
- # Rename the folders
- try:
- os.rename(longest_folder, axial_path)
- print(f"Renamed '{longest_folder}' to '{axial_path}'")
- except FileExistsError:
- print(f"Cannot rename '{longest_folder}' to '{axial_path}': Destination already exists.")
- except Exception as e:
- print(f"Error renaming '{longest_folder}' to '{axial_path}': {e}")
- try:
- os.rename(shortest_folder, sagittal_path)
- print(f"Renamed '{shortest_folder}' to '{sagittal_path}'")
- except FileExistsError:
- print(f"Cannot rename '{shortest_folder}' to '{sagittal_path}': Destination already exists.")
- except Exception as e:
- print(f"Error renaming '{shortest_folder}' to '{sagittal_path}': {e}")
- # %%
- # check the lenght of each folder
- import os
- root_folder = r"D:\AISSLab\Code\3D CNN\datasets\test_system\Dicom"
- sagittal_counts = []
- for patient_name in os.listdir(root_folder):
- patient_folder = os.path.join(root_folder, patient_name)
- if not os.path.isdir(patient_folder):
- continue
- for item in os.listdir(patient_folder):
- item_path = os.path.join(patient_folder, item)
- if os.path.isdir(item_path):
- sagittal_path = os.path.join(item_path, "Sagittal")
- if os.path.isdir(sagittal_path):
- file_count = sum(len(files) for _, _, files in os.walk(sagittal_path))
- sagittal_counts.append((sagittal_path, file_count))
- # Sort and get top 5
- top5_sagittal = sorted(sagittal_counts, key=lambda x: x[1], reverse=True)[:10]
- # Display results
- print("Top 5 Sagittal directories with the largest number of files:")
- for path, count in top5_sagittal:
- print(f"{path} - {count} files")
- # %% [markdown]
- # ## padding
- # %%
- import os
- import pydicom
- import numpy as np
- from pydicom.uid import generate_uid
- def pad_dicom_series(folder_path, target_count=18):
- # Load and sort DICOM files by InstanceNumber
- dicom_files = sorted(
- [f for f in os.listdir(folder_path) if f.lower().endswith('.dcm')],
- key=lambda x: int(pydicom.dcmread(os.path.join(folder_path, x)).InstanceNumber)
- )
- current_count = len(dicom_files)
- if current_count >= target_count:
- print(f"{folder_path} already has {current_count} slices.")
- return
- print(f"Padding {folder_path}: {current_count} → {target_count}")
- last_file = os.path.join(folder_path, dicom_files[-1])
- last_ds = pydicom.dcmread(last_file)
- last_instance_number = int(last_ds.InstanceNumber)
- # Determine slice spacing
- if current_count >= 2:
- second_last_file = os.path.join(folder_path, dicom_files[-2])
- second_last_ds = pydicom.dcmread(second_last_file)
- spacing = np.array(last_ds.ImagePositionPatient) - np.array(second_last_ds.ImagePositionPatient)
- else:
- spacing = np.array([0, 0, 1]) # default spacing if only 1 slice
- current_position = np.array(last_ds.ImagePositionPatient)
- rows, cols = last_ds.Rows, last_ds.Columns
- dtype = last_ds.pixel_array.dtype
- black_image = np.zeros((rows, cols), dtype=dtype).tobytes()
- instance_number = last_instance_number # starting point
- for i in range(target_count - current_count):
- instance_number += 1 # increment correctly
- new_ds = last_ds.copy()
- new_ds.SOPInstanceUID = generate_uid()
- new_ds.InstanceNumber = instance_number
- # Update position
- new_position = current_position + spacing * (i + 1)
- new_ds.ImagePositionPatient = [str(p) for p in new_position]
- if 'SliceLocation' in new_ds:
- new_ds.SliceLocation = float(new_ds.SliceLocation) + spacing[-1] * (i + 1)
- new_ds.PixelData = black_image
- # Save
- filename = os.path.join(folder_path, f"pad_{i+1:03d}.dcm")
- new_ds.save_as(filename)
- print("✅ Padding complete and InstanceNumbers correctly incremented.")
- # Example usage
- # folder = r"Sagittal"
- # pad_dicom_series(folder)
- # %%
- root_folder = r"D:\AISSLab\Code\3D CNN\datasets\test_system\Dicom"
- for patient_folder in os.listdir(root_folder):
- patient_folder = os.path.join(root_folder ,patient_folder)
- for subfolders in os.listdir(patient_folder):
- if os.path.isdir( os.path.join(patient_folder ,subfolders)):
- for sagittal in os.listdir( os.path.join(patient_folder ,subfolders)):
- if sagittal == "Sagittal":
- print(os.path.join(patient_folder ,subfolders,sagittal))
- pad_dicom_series(os.path.join(patient_folder ,subfolders,sagittal))
- # %% [markdown]
- # copy the padding image to other folder
- # %%
- import os
- import shutil
- root_folder = r"D:\AISSLab\Code\3D CNN\datasets\DatasetV0.17 Dicom"
- destination_base = r"preprocessing_Dataset"
- for patient_folder in os.listdir(root_folder):
- patient_folder_path = os.path.join(root_folder, patient_folder)
- if not os.path.isdir(patient_folder_path):
- continue
- for subfolder in os.listdir(patient_folder_path):
- subfolder_path = os.path.join(patient_folder_path, subfolder)
- if not os.path.isdir(subfolder_path):
- continue
- for item in os.listdir(subfolder_path):
- if item == "Sagittal":
- sagittal_path = os.path.join(subfolder_path, item)
- print(f"Found Sagittal folder: {sagittal_path}")
- # Create destination directory
- dest_dir = os.path.join(destination_base, patient_folder)
- os.makedirs(dest_dir, exist_ok=True)
- # Copy all files from Sagittal folder
- for file in os.listdir(sagittal_path):
- src_file = os.path.join(sagittal_path, file)
- if os.path.isfile(src_file):
- shutil.copy2(src_file, os.path.join(dest_dir, file))
- print(f"✅ Copied to {dest_dir}")
- # %% [markdown]
- # labeling data
- # %%
- import pandas as pd
- import xml.etree.ElementTree as ET
- # %%
- # root_dir = r"D:\AISSLab\Code\3D CNN\datasets\DatasetV0.21 Final"
- root_dir = r"D:\Submitted Matrial (conference&journal)\Sagittal Data Artical\V0.47 Dataset analysis\DatasetV0.47 Final\DatasetV0.47"
- df= pd.DataFrame(columns = ["patient_ID","filename","level","name", "xmin","ymin","xmax","ymax" ,"width","height"])
- for patient_ in os.listdir(root_dir):
- patient_folder = os.path.join(root_dir, patient_)
- for sag in os.listdir(patient_folder):
- if sag =="Sagittal":
- sagittal_folder = os.path.join(patient_folder, sag)
- for XML in os.listdir(sagittal_folder):
- if XML.endswith("xml"):
- xml_path = os.path.join(sagittal_folder, XML)
- # print(patient_)
- # print(XML)
- # Load the XML file
- tree = ET.parse(xml_path) # Replace with the path to your XML file
- root = tree.getroot()
- # Extract global information
- filename = root.find('filename').text
- width = int(root.find('size/width').text)
- height = int(root.find('size/height').text)
- # Extract all objects
- data = []
- for obj in root.findall('object'):
- level = obj.find('level').text
- name = obj.find('name').text
- bbox = obj.find('bndbox')
- xmin = int(bbox.find('xmin').text)
- ymin = int(bbox.find('ymin').text)
- xmax = int(bbox.find('xmax').text)
- ymax = int(bbox.find('ymax').text)
- new_row = {
- "patient_ID":patient_,
- 'filename': XML.replace(".xml" , ""),
- 'level': level,
- 'name': name,
- 'xmin': xmin,
- 'ymin': ymin,
- 'xmax': xmax,
- 'ymax': ymax,
- 'width': width,
- 'height': height
- }
- df.loc[len(df)] = new_row
- # %%
- df.to_csv("label.csv" , index=False)
- # %%
- df
- # %%
- # df= pd.DataFrame(columns = ["patient_ID","level","name", "xmin","ymin","xmax","ymax" ,"width","height"])
- # %%
- # # Define a new row as a dictionary
- # new_row = {
- # 'filename': 'IM000004.png',
- # 'level': 'L3-L4',
- # 'name': 'LFS3',
- # 'xmin': 250,
- # 'ymin': 300,
- # 'xmax': 310,
- # 'ymax': 360,
- # 'width': 576,
- # 'height': 576
- # }
- # # Add it to the DataFrame
- # df.loc[len(df)] = new_row
- # # Show the updated DataFrame
- # print(df)
- # %% [markdown]
- # ### labeling
- # %%
- # old without consider the repetation of boxes
- # import pandas as pd
- # import json
- # import os
- # from collections import defaultdict
- # # Load dataframe
- # df = pd.read_csv("label.csv", sep=",")
- # # Normalize center
- # def compute_center(row):
- # x_center = (row["xmin"] + row["xmax"]) / 2 / row["width"]
- # y_center = (row["ymin"] + row["ymax"]) / 2 / row["height"]
- # return x_center, y_center
- # # Track z count
- # z_tracker = defaultdict(lambda: defaultdict(lambda: defaultdict(int)))
- # output_dir = r"D:\AISSLab\Code\3D CNN\datasets\label"
- # os.makedirs(output_dir, exist_ok=True)
- # patient_jsons = {}
- # i = 0
- # for patient_id, group in df.groupby("patient_ID"):
- # result = {
- # "L1-L2": {"left": None, "right": None},
- # "L2-L3": {"left": None, "right": None},
- # "L3-L4": {"left": None, "right": None},
- # "L4-L5": {"left": None, "right": None},
- # "L5-S1": {"left": None, "right": None},
- # }
- # repetation = []
- # for _, row in group.iterrows():
- # level = row["level"]
- # side = "left" if row["name"].startswith("LFS") else "right"
- # x, y = compute_center(row)
- # index_slice = row["filename"]
- # z= index_slice.replace("IM0000" , "")
- # if z[0] =="0" :
- # try:
- # z=int(z.replace("0",""))
- # except:
- # pass
- # else:
- # try:
- # z=int(z)
- # except:
- # pass
- # z = int(z) / 18
- # result[level][side] = [round(x, 4), round(y, 4), round(z, 4)]
- # patient_jsons[patient_id] = result
- # # Save per patient
- # file_path = os.path.join(output_dir, f"{patient_id}.json")
- # with open(file_path, "w") as f:
- # json.dump(result, f, indent=2)
- # %%
- # with consideration repetation
- import pandas as pd
- import json
- import os
- from collections import defaultdict
- from collections import Counter
- # Load dataframe
- df = pd.read_csv("label.csv", sep=",")
- # Normalize center
- def compute_center(row):
- x_center = (row["xmin"] + row["xmax"]) / 2 / row["width"]
- y_center = (row["ymin"] + row["ymax"]) / 2 / row["height"]
- return x_center, y_center
- # Track z count
- z_tracker = defaultdict(lambda: defaultdict(lambda: defaultdict(int)))
- output_dir = r"labelv1"
- os.makedirs(output_dir, exist_ok=True)
- patient_jsons = {}
- i = 0
- for patient_id, group in df.groupby("patient_ID"):
- result = {
- "L1-L2": {"left": None, "right": None},
- "L2-L3": {"left": None, "right": None},
- "L3-L4": {"left": None, "right": None},
- "L4-L5": {"left": None, "right": None},
- "L5-S1": {"left": None, "right": None},
- }
- repetation = []
- for _, row in group.iterrows():
- try:
- level = row["level"]
- side = "left" if row["name"].startswith("LFS") else "right"
- x, y = compute_center(row)
- index_slice = row["filename"]
- z= index_slice.replace("IM0000" , "")
- if z[0] =="0" :
- try:
- z=int(z.replace("0",""))
- except:
- pass
- else:
- try:
- z=int(z)
- except:
- pass
- z = int(z) / 18
- repetation.append([level, side ,index_slice, x, y , z])
- key_pairs = [(item[0], item[1]) for item in repetation]
- # Count repetitions
- counts = Counter(key_pairs)
- # Print repeated pairs
- for pair, count in counts.items():
- if count > 1:
- target = pair
- indices = [i for i, item in enumerate(repetation) if item[0] == target[0] and item[1] == target[1]]
- # print(repetation)
- repetation_times_1 = repetation[indices[0]][2]
- repetation_times_2 = repetation[indices[1]][2]
- count_1 = sum(1 for row in repetation if repetation_times_1 in row)
- count_2 = sum(1 for row in repetation if repetation_times_2 in row)
- if count_1 > count_2 :
- "delete list of two "
- del repetation[indices[1]]
- else:
- "delete repetation one "
- del repetation[indices[0]]
- for level, side, _, x, y, z in repetation:
- if level in result and side in result[level]:
- result[level][side] = (round(x,4), round(y,4),round( z, 4) )
- except:
- pass
- # Save per patient
- file_path = os.path.join(output_dir, f"{patient_id}.json")
- with open(file_path, "w") as f:
- json.dump(result, f, indent=2)
position_of_slices.ipynb at commit 4a8c597, no license · at the source
Overview
- Department of Artificial Intelligence and Data Science, College of AI Convergence, Daeyang AI Center, Sejong University,Seoul, 05006 Korea
- Department of Neurosurgery, Faculty of Medicine, Fırat University,Elazığ, Turkey
- Department of Computer Engineering, Faculty of Engineering, Fırat University,Elazığ, Turkey
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.
AISSLab2025/LSS-MRI-AISSLab-Dataset
4a8c5972fbb81be86e038723c57f941e6efb8f92, 19 May 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
9 files
- de_identification.py, Python, 69 lines, 1 match
- models/
Custom_CNN.ipynb , Jupyter, 699 lines, 2 matches - models/
Diet_model.ipynb , Jupyter, 298 lines, 2 matches - models/
Ensamble_Diet_Custom_CNN , Jupyter, 219 lines.ipynb - models/
ROI_detection_YOLO.ipynb , Jupyter, 243 lines - models/
Slection_selection_testi , Jupyter, 328 linesng.ipynb - models/
Slice_slection_training. , Jupyter, 529 linesipynb - models/
position_of_slices.ipynb , Jupyter, 509 lines, 2 matches - README.md, Text, 154 lines
Code availability statement
The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: AISSLab2025/
LSS-MRI-AISSLab-Dataset
Read it in the paper: doi.org/10.1038/s41597-026-07138-x.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 8 scripts, each with its path and the digest of its content;
- 7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- doi:10.17632/
k57fr854j2.2 , at the source; found in the references - doi:10.17632/
rgb77xm3jf.4 , at the source; found in “Data availability” - doi:10.17632/
x6ggzp2ycn.1 , at the source; found in the references
Data availability statement
The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to a dataset: DOI 10.17632/
rgb77xm3jf.4
Read it in the paper: doi.org/10.1038/s41597-026-07138-x.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 5 MeSH terms, 3 funders, 44 references.
Cite
This paper
Abdulmahmod, O. F., Al-antari, M. A., Kwon, H., Habib, A., Raza, M., Kaplan, M., Ertuğrul, B., Akçin, İ., Bütün, E., & Gu, Y. H. (2026). Medical Spine Sagittal MRI Dataset for Segmentation and Foraminal Stenosis detection. Scientific data, 13(1), 809. https://
BibTeX
@article{abdulmahmod2026
author = {Abdulmahmod, Osamah F. and Al-antari, Mugahed A. and Kwon, Hyunwook and Habib, Afnan and Raza, Mukhlis and Kaplan, Metin and Ertuğrul, Bilal and Akçin, İsmail and Bütün, Ertan and Gu, Yeong Hyeon},
title = {{Medical Spine Sagittal MRI Dataset for Segmentation and Foraminal Stenosis detection}},
journal = {Scientific data},
year = {2026},
month = apr,
volume = {13},
number = {1},
pages = {809},
publisher = {Nature Publishing Group},
issn = {2052-4463},
doi = {10.1038/
url = {https://
pmid = {41957051},
pmcid = {PMC13222877}
}
RIS
TY - JOUR
AU - Abdulmahmod, Osamah F.
AU - Al-antari, Mugahed A.
AU - Kwon, Hyunwook
AU - Habib, Afnan
AU - Raza, Mukhlis
AU - Kaplan, Metin
AU - Ertuğrul, Bilal
AU - Akçin, İsmail
AU - Bütün, Ertan
AU - Gu, Yeong Hyeon
TI - Medical Spine Sagittal MRI Dataset for Segmentation and Foraminal Stenosis detection
T2 - Scientific data
J2 - Sci Data
PY - 2026
DA - 2026/
VL - 13
IS - 1
SP - 809
SN - 2052-4463
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"id": "10.1038/
"type": "article-journal",
"title": "Medical Spine Sagittal MRI Dataset for Segmentation and Foraminal Stenosis detection",
"container-title": "Scientific data",
"author": [
{
"family": "Abdulmahmod",
"given": "Osamah F."
},
{
"family": "Al-antari",
"given": "Mugahed A."
},
{
"family": "Kwon",
"given": "Hyunwook"
},
{
"family": "Habib",
"given": "Afnan"
},
{
"family": "Raza",
"given": "Mukhlis"
},
{
"family": "Kaplan",
"given": "Metin"
},
{
"family": "Ertuğrul",
"given": "Bilal"
},
{
"family": "Akçin",
"given": "İsmail"
},
{
"family": "Bütün",
"given": "Ertan"
},
{
"family": "Gu",
"given": "Yeong Hyeon"
}
],
"container-title-short":
"volume": "13",
"issue": "1",
"page": "809",
"DOI": "10.1038/
"PMID": "41957051",
"PMCID": "PMC13222877",
"ISSN": "2052-4463",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
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9
]
]
}
}
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