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  3. 2003.04696
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TorchIO: A Python library for efficient loading, preprocessing,
  augmentation and patch-based sampling of medical images in deep learning
v1v2v3v4v5 (latest)

TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning

9 March 2020
Fernando Pérez-García
Rachel Sparks
Sébastien Ourselin
    MedImLM&MA
ArXiv (abs)PDFHTML

Papers citing "TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning"

50 / 158 papers shown
Retrospective motion correction in MRI using disentangled embeddings
Retrospective motion correction in MRI using disentangled embeddings
Qi Wang
Veronika Ecker
Marcel Früh
S. Gatidis
Thomas Kustner
126
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11 Nov 2025
Optimizing the nnU-Net model for brain tumor (Glioma) segmentation Using a BraTS Sub-Saharan Africa (SSA) dataset
Optimizing the nnU-Net model for brain tumor (Glioma) segmentation Using a BraTS Sub-Saharan Africa (SSA) dataset
Chukwuemeka Arua Kalu
Adaobi Chiazor Emegoakor
Fortune Okafor
Augustine Okoh Uchenna
Chijioke Kelvin Ukpai
Godsent Erere Onyeugbo
168
0
0
04 Nov 2025
Stroke Lesion Segmentation in Clinical Workflows: A Modular, Lightweight, and Deployment-Ready Tool
Stroke Lesion Segmentation in Clinical Workflows: A Modular, Lightweight, and Deployment-Ready Tool
Yann Kerverdo
Florent Leray
Youwan Mahé
Stéphanie Leplaideur
Francesca Galassi
99
0
0
28 Oct 2025
Comprehensive language-image pre-training for 3D medical image understanding
Comprehensive language-image pre-training for 3D medical image understanding
Tassilo Wald
Ibrahim Ethem Hamamci
Yuan Gao
Sam Bond-Taylor
H. Sharma
...
Panagiotis Korfiatis
Valentina Salvatelli
Javier Alvarez-Valle
Fernando Pérez-García
Fernando Pérez-García
MedImVLM
257
2
0
16 Oct 2025
Rewiring Development in Brain Segmentation: Leveraging Adult Brain Priors for Enhancing Infant MRI Segmentation
Rewiring Development in Brain Segmentation: Leveraging Adult Brain Priors for Enhancing Infant MRI Segmentation
Alemu Sisay Nigru
M. Svanera
Austin Dibble
Connor Dalby
Mattia Savardi
Sergio Benini
104
0
0
10 Oct 2025
How We Won BraTS-SSA 2025: Brain Tumor Segmentation in the Sub-Saharan African Population Using Segmentation-Aware Data Augmentation and Model Ensembling
How We Won BraTS-SSA 2025: Brain Tumor Segmentation in the Sub-Saharan African Population Using Segmentation-Aware Data Augmentation and Model Ensembling
Claudia Takyi Ankomah
Livingstone Eli Ayivor
Ireneaus Nyame
Leslie Wambo
Patrick Yeboah Bonsu
Aondona Moses Iorumbur
Raymond Confidence
Toufiq Musah
208
0
0
03 Oct 2025
Robust Fetal Pose Estimation across Gestational Ages via Cross-Population Augmentation
Robust Fetal Pose Estimation across Gestational Ages via Cross-Population AugmentationInternational Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025
Sebastian Diaz
Benjamin Billot
Neel Dey
Molin Zhang
Esra Abaci Turk
P. E. Grant
Polina Golland
E. Adalsteinsson
134
2
0
15 Sep 2025
Systematic Review and Meta-analysis of AI-driven MRI Motion Artifact Detection and Correction
Systematic Review and Meta-analysis of AI-driven MRI Motion Artifact Detection and Correction
Mojtaba Safari
Zach Eidex
Richard L. J. Qiu
Matthew Goette
Tonghe Wang
Xiaofeng Yang
MedIm
140
1
0
05 Sep 2025
Mask-Guided Multi-Channel SwinUNETR Framework for Robust MRI Classification
Mask-Guided Multi-Channel SwinUNETR Framework for Robust MRI Classification
Smriti Joshi
Lidia Garrucho
Richard Osuala
Oliver Díaz
Karim Lekadir
OOD
98
0
0
28 Aug 2025
UNISELF: A Unified Network with Instance Normalization and Self-Ensembled Lesion Fusion for Multiple Sclerosis Lesion Segmentation
UNISELF: A Unified Network with Instance Normalization and Self-Ensembled Lesion Fusion for Multiple Sclerosis Lesion Segmentation
Jinwei Zhang
Lianrui Zuo
Blake E. Dewey
Samuel W. Remedios
Yihao Liu
...
E. Mowry
S. Newsome
P. Calabresi
A. Carass
Jerry L. Prince
187
4
0
06 Aug 2025
MRpro - open PyTorch-based MR reconstruction and processing package
MRpro - open PyTorch-based MR reconstruction and processing package
F. Zimmermann
Patrick Schuenke
Christoph S. Aigner
Bill A. Bernhardt
Mara Guastini
...
Catarina Redshaw Kranich
Jakob Schattenfroh
David Schote
Yanglei Wu
C. Kolbitsch
172
1
0
30 Jul 2025
Learning from Heterogeneous Structural MRI via Collaborative Domain Adaptation for Late-Life Depression Assessment
Learning from Heterogeneous Structural MRI via Collaborative Domain Adaptation for Late-Life Depression Assessment
Yuzhen Gao
Qianqian Wang
Yongheng Sun
C. Wang
Yongquan Liang
Mingxia Liu
203
0
0
30 Jul 2025
trAIce3D: A Prompt-Driven Transformer Based U-Net for Semantic Segmentation of Microglial Cells from Large-Scale 3D Microscopy Images
trAIce3D: A Prompt-Driven Transformer Based U-Net for Semantic Segmentation of Microglial Cells from Large-Scale 3D Microscopy Images
MohammadAmin Alamalhoda
Arsalan Firoozi
Alessandro Venturino
Sandra Siegert
MedIm
137
0
0
30 Jul 2025
Extreme Cardiac MRI Analysis under Respiratory Motion: Results of the CMRxMotion Challenge
Extreme Cardiac MRI Analysis under Respiratory Motion: Results of the CMRxMotion Challenge
Kang Wang
C. Qin
Zhang Shi
Haoran Wang
X. Zhang
...
Xinrong Chen
He Wang
Chengyan Wang
Wenjia Bai
S. Wang
226
5
0
25 Jul 2025
RealKeyMorph: Keypoints in Real-world Coordinates for Resolution-agnostic Image Registration
RealKeyMorph: Keypoints in Real-world Coordinates for Resolution-agnostic Image Registration
Mina C Moghadam
Alan Q. Wang
Omer Taub
Martin R. Prince
M. Sabuncu
310
0
0
12 Jun 2025
Estimation of Head Motion in Structural MRI and its Impact on Cortical Thickness Measurements in Retrospective Data
Estimation of Head Motion in Structural MRI and its Impact on Cortical Thickness Measurements in Retrospective Data
Charles Bricout
Samira Ebrahimi Kahou
Sylvain Bouix
MedIm
162
0
0
29 May 2025
Towards One-shot Federated Learning: Advances, Challenges, and Future Directions
Towards One-shot Federated Learning: Advances, Challenges, and Future Directions
Flora Amato
Lingyu Qiu
Mohammad Tanveer
S. Cuomo
F. Giampaolo
F. Piccialli
FedML
451
4
0
05 May 2025
Lightweight Medical Image Restoration via Integrating Reliable Lesion-Semantic Driven Prior
Lightweight Medical Image Restoration via Integrating Reliable Lesion-Semantic Driven Prior
Pengcheng Zheng
Kecheng Chen
Jiaxin Huang
Bohao Chen
Ju Liu
Yazhou Ren
X. Pu
MedIm
311
1
0
15 Apr 2025
Conformalized Generative Bayesian Imaging: An Uncertainty Quantification Framework for Computational Imaging
Conformalized Generative Bayesian Imaging: An Uncertainty Quantification Framework for Computational Imaging
Canberk Ekmekci
Müjdat Çetin
UQCVMedIm
426
5
0
10 Apr 2025
IterMask3D: Unsupervised Anomaly Detection and Segmentation with Test-Time Iterative Mask Refinement in 3D Brain MR
IterMask3D: Unsupervised Anomaly Detection and Segmentation with Test-Time Iterative Mask Refinement in 3D Brain MRMedical Image Analysis (MedIA), 2025
Ziyun Liang
Xiaoqing Guo
Wentian Xu
Yasin Ibrahim
Natalie Voets
Pieter M Pretorius
J. A. Noble
Konstantinos Kamnitsas
336
2
0
07 Apr 2025
QuickDraw: Fast Visualization, Analysis and Active Learning for Medical Image Segmentation
QuickDraw: Fast Visualization, Analysis and Active Learning for Medical Image SegmentationInteracción (HCII), 2025
Daniel Syomichev
Padmini Gopinath
Guang-Lin Wei
Eric Chang
Ian Gordon
Amanuel Seifu
Rahul Pemmaraju
Neehar Peri
James M. Purtilo
342
1
0
12 Mar 2025
Integration of nested cross-validation, automated hyperparameter optimization, high-performance computing to reduce and quantify the variance of test performance estimation of deep learning models
Integration of nested cross-validation, automated hyperparameter optimization, high-performance computing to reduce and quantify the variance of test performance estimation of deep learning models
Paul Calle
Averi Bates
Justin C Reynolds
Yunlong Liu
Haoyang Cui
...
Alberto J. de Armendi
Shashank S. Shettar
Kar Ming Fung
Qinggong Tang
Chongle Pan
345
10
0
11 Mar 2025
A cautionary tale on the cost-effectiveness of collaborative AI in
  real-world medical applications
A cautionary tale on the cost-effectiveness of collaborative AI in real-world medical applicationsbioRxiv (bioRxiv), 2024
Francesco Cremonesi
Lucia Innocenti
Sebastien Ourselin
Vicky Goh
Michela Antonelli
Marco Lorenzi
FedML
340
0
0
09 Dec 2024
Medical Slice Transformer: Improved Diagnosis and Explainability on 3D
  Medical Images with DINOv2
Medical Slice Transformer: Improved Diagnosis and Explainability on 3D Medical Images with DINOv2
Gustav Muller-Franzes
Firas Khader
R. Siepmann
T. Han
Jakob Nikolas Kather
S. Nebelung
Daniel Truhn
MedIm
470
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24 Nov 2024
De-Identification of Medical Imaging Data: A Comprehensive Tool for
  Ensuring Patient Privacy
De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient PrivacyEuropean Radiology (Eur Radiol), 2024
Moritz Rempe
Lukas Heine
C. Seibold
Fabian Horst
Jens Kleesiek
MedIm
226
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16 Oct 2024
DyMix: Dynamic Frequency Mixup Scheduler based Unsupervised Domain
  Adaptation for Enhancing Alzheimer's Disease Identification
DyMix: Dynamic Frequency Mixup Scheduler based Unsupervised Domain Adaptation for Enhancing Alzheimer's Disease Identification
Yooseung Shin
Kwanseok Oh
Heung-Il Suk
302
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MCDDPM: Multichannel Conditional Denoising Diffusion Model for
  Unsupervised Anomaly Detection in Brain MRI
MCDDPM: Multichannel Conditional Denoising Diffusion Model for Unsupervised Anomaly Detection in Brain MRI
Vivek Kumar Trivedi
Bheeshm Sharma
P. Balamurugan
DiffMMedIm
300
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29 Sep 2024
deepmriprep: Voxel-based Morphometry (VBM) Preprocessing via Deep Neural
  Networks
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L. Fisch
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Earth System Data Cubes: Avenues for advancing Earth system research
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David Montero
Guido Kraemer
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Gunnar Brandt
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Martin Reinhardt
Maximilian Sochting
Khalil Teber
Miguel D. Mahecha
311
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05 Aug 2024
A Federated Learning-Friendly Approach for Parameter-Efficient
  Fine-Tuning of SAM in 3D Segmentation
A Federated Learning-Friendly Approach for Parameter-Efficient Fine-Tuning of SAM in 3D Segmentation
Mothilal Asokan
Difei Gao
Joya Chen
Mike Zheng Shou
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367
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31 Jul 2024
Force Sensing Guided Artery-Vein Segmentation via Sequential Ultrasound
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Yimeng Geng
Gaofeng Meng
Ya-Ting Chan
Guanglin Cao
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Quantitative Evaluation of the Saliency Map for Alzheimer's Disease
  Classifier with Anatomical Segmentation
Quantitative Evaluation of the Saliency Map for Alzheimer's Disease Classifier with Anatomical Segmentation
Yihan Zhang
Xuanshuo Zhang
Wei Wu
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237
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11 Jul 2024
Automated MRI Quality Assessment of Brain T1-weighted MRI in Clinical
  Data Warehouses: A Transfer Learning Approach Relying on Artefact Simulation
Automated MRI Quality Assessment of Brain T1-weighted MRI in Clinical Data Warehouses: A Transfer Learning Approach Relying on Artefact Simulation
Sophie Loizillon
Simona Bottani
Stéphane Mabille
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Sebastian Ströer
Didier Dormont
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232
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18 Jun 2024
Comparative Benchmarking of Failure Detection Methods in Medical Image
  Segmentation: Unveiling the Role of Confidence Aggregation
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M. Zenk
David Zimmerer
Hyunjin Park
Jeremias Traub
T. Norajitra
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Klaus H. Maier-Hein
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Patch-Based Encoder-Decoder Architecture for Automatic Transmitted Light
  to Fluorescence Imaging Transition: Contribution to the LightMyCells
  Challenge
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Marek Wodzinski
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ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency
  to facilitate Artificial Intelligence applications from acquisition to
  analysis in Magnetic Resonance Imaging
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D. Karkalousos
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A Universal Metric of Dataset Similarity for Cross-silo Federated Learning
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Automatic Cranial Defect Reconstruction with Self-Supervised Deep
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Deep Learning-Based Segmentation of Tumors in PET/CT Volumes: Benchmark
  of Different Architectures and Training Strategies
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Monika Górka
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Artifact Reduction in 3D and 4D Cone-beam Computed Tomography Images
  with Deep Learning -- A Review
Artifact Reduction in 3D and 4D Cone-beam Computed Tomography Images with Deep Learning -- A Review
Mohammadreza Amirian
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Iterative Learning for Joint Image Denoising and Motion Artifact
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Lintao Zhang
Mengqi Wu
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wmh_seg: Transformer based U-Net for Robust and Automatic White Matter
  Hyperintensity Segmentation across 1.5T, 3T and 7T
wmh_seg: Transformer based U-Net for Robust and Automatic White Matter Hyperintensity Segmentation across 1.5T, 3T and 7T
Jinghang Li
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Howard J. Aizenstein
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139
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DeepCERES: A Deep learning method for cerebellar lobule segmentation
  using ultra-high resolution multimodal MRI
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Sergio Morell-Ortega
Marina Ruiz-Perez
Marien Gadea
Roberto Vivó Hernando
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F. Aparici-Robles
M. Iglesia-Vayá
G. Catheline
Pierrick Coupé
J. V. Manjón
259
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22 Jan 2024
DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI
DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI
Marina Ruiz-Perez
Sergio Morell-Ortega
Marien Gadea
Roberto Vivó Hernando
Gregorio Rubio
F. Aparici-Robles
M. Iglesia-Vayá
T. Tourdias
Pierrick Coupé
J. V. Manjón
300
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Continual Learning in Medical Image Analysis: A Comprehensive Review of
  Recent Advancements and Future Prospects
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Pratibha Kumari
Joohi Chauhan
Afshin Bozorgpour
Boqiang Huang
Reza Azad
Dorit Merhof
462
28
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28 Dec 2023
PULASki: Learning inter-rater variability using statistical distances to improve probabilistic segmentation
PULASki: Learning inter-rater variability using statistical distances to improve probabilistic segmentation
S. Chatterjee
Franziska Gaidzik
Alessandro Sciarra
Hendrik Mattern
G. Janiga
Oliver Speck
Andreas Nürnberger
S. Pathiraja
351
0
0
25 Dec 2023
SE(3)-Equivariant and Noise-Invariant 3D Rigid Motion Tracking in Brain
  MRI
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Benjamin Billot
Neel Dey
Daniel Moyer
M. Hoffmann
Esra Abaci Turk
B. Gagoski
Ellen Grant
Polina Golland
3DPC
497
11
0
21 Dec 2023
MRI Scan Synthesis Methods based on Clustering and Pix2Pix
MRI Scan Synthesis Methods based on Clustering and Pix2PixConference on Artificial Intelligence in Medicine in Europe (AIME), 2023
Giulia Baldini
Melanie Schmidt
Charlotte Zäske
Liliana L. Caldeira
246
8
0
08 Dec 2023
Shape-aware Segmentation of the Placenta in BOLD Fetal MRI Time Series
Shape-aware Segmentation of the Placenta in BOLD Fetal MRI Time Series
S. M. Abulnaga
Neel Dey
Sean I. Young
Eileen Pan
Katherine I. Hobgood
Clinton Jia Wang
P. E. Grant
Esra Abaci Turk
Polina Golland
251
5
0
08 Dec 2023
Guided Reconstruction with Conditioned Diffusion Models for Unsupervised Anomaly Detection in Brain MRIs
Guided Reconstruction with Conditioned Diffusion Models for Unsupervised Anomaly Detection in Brain MRIs
F. Behrendt
Debayan Bhattacharya
R. Mieling
Lennart Maack
Julia Kruger
R. Opfer
Alexander Schlaefer
DiffMMedIm
458
23
0
07 Dec 2023
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