Transformers for Neuroimage Segmentation: Scoping Review
BackgroundNeuroimaging segmentation is increasingly important for diagnosing and planning treatments for neurological diseases. Manual segmentation is time-consuming, apart from being prone to human error and variability. Transformers are a promising deep learning approach fo...
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JMIR Publications
2025-01-01
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| Series: | Journal of Medical Internet Research |
| Online Access: | https://www.jmir.org/2025/1/e57723 |
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| author | Maya Iratni Amira Abdullah Mariam Aldhaheri Omar Elharrouss Alaa Abd-alrazaq Zahiriddin Rustamov Nazar Zaki Rafat Damseh |
| author_facet | Maya Iratni Amira Abdullah Mariam Aldhaheri Omar Elharrouss Alaa Abd-alrazaq Zahiriddin Rustamov Nazar Zaki Rafat Damseh |
| author_sort | Maya Iratni |
| collection | DOAJ |
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BackgroundNeuroimaging segmentation is increasingly important for diagnosing and planning treatments for neurological diseases. Manual segmentation is time-consuming, apart from being prone to human error and variability. Transformers are a promising deep learning approach for automated medical image segmentation.
ObjectiveThis scoping review will synthesize current literature and assess the use of various transformer models for neuroimaging segmentation.
MethodsA systematic search in major databases, including Scopus, IEEE Xplore, PubMed, and ACM Digital Library, was carried out for studies applying transformers to neuroimaging segmentation problems from 2019 through 2023. The inclusion criteria allow only for peer-reviewed journal papers and conference papers focused on transformer-based segmentation of human brain imaging data. Excluded are the studies dealing with nonneuroimaging data or raw brain signals and electroencephalogram data. Data extraction was performed to identify key study details, including image modalities, datasets, neurological conditions, transformer models, and evaluation metrics. Results were synthesized using a narrative approach.
ResultsOf the 1246 publications identified, 67 (5.38%) met the inclusion criteria. Half of all included studies were published in 2022, and more than two-thirds used transformers for segmenting brain tumors. The most common imaging modality was magnetic resonance imaging (n=59, 88.06%), while the most frequently used dataset was brain tumor segmentation dataset (n=39, 58.21%). 3D transformer models (n=42, 62.69%) were more prevalent than their 2D counterparts. The most developed were those of hybrid convolutional neural network-transformer architectures (n=57, 85.07%), where the vision transformer is the most frequently used type of transformer (n=37, 55.22%). The most frequent evaluation metric was the Dice score (n=63, 94.03%). Studies generally reported increased segmentation accuracy and the ability to model both local and global features in brain images.
ConclusionsThis review represents the recent increase in the adoption of transformers for neuroimaging segmentation, particularly for brain tumor detection. Currently, hybrid convolutional neural network-transformer architectures achieve state-of-the-art performances on benchmark datasets over standalone models. Nevertheless, their applicability remains highly limited by high computational costs and potential overfitting on small datasets. The heavy reliance of the field on the brain tumor segmentation dataset hints at the use of a more diverse set of datasets to validate the performances of models on a variety of neurological diseases. Further research is needed to define the optimal transformer architectures and training methods for clinical applications. Continuing development may make transformers the state-of-the-art for fast, accurate, and reliable brain magnetic resonance imaging segmentation, which could lead to improved clinical tools for diagnosing and evaluating neurological disorders. |
| format | Article |
| id | doaj-art-47f5ef5d679d4c43800fb0fc2d87d319 |
| institution | Kabale University |
| issn | 1438-8871 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | JMIR Publications |
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| series | Journal of Medical Internet Research |
| spelling | doaj-art-47f5ef5d679d4c43800fb0fc2d87d3192025-01-29T17:00:39ZengJMIR PublicationsJournal of Medical Internet Research1438-88712025-01-0127e5772310.2196/57723Transformers for Neuroimage Segmentation: Scoping ReviewMaya Iratnihttps://orcid.org/0000-0002-3567-7885Amira Abdullahhttps://orcid.org/0000-0001-9896-5676Mariam Aldhaherihttps://orcid.org/0009-0005-8901-4242Omar Elharrousshttps://orcid.org/0000-0002-5341-5440Alaa Abd-alrazaqhttps://orcid.org/0000-0001-7695-4626Zahiriddin Rustamovhttps://orcid.org/0000-0003-4977-1781Nazar Zakihttps://orcid.org/0000-0002-6259-9843Rafat Damsehhttps://orcid.org/0000-0001-6797-0448 BackgroundNeuroimaging segmentation is increasingly important for diagnosing and planning treatments for neurological diseases. Manual segmentation is time-consuming, apart from being prone to human error and variability. Transformers are a promising deep learning approach for automated medical image segmentation. ObjectiveThis scoping review will synthesize current literature and assess the use of various transformer models for neuroimaging segmentation. MethodsA systematic search in major databases, including Scopus, IEEE Xplore, PubMed, and ACM Digital Library, was carried out for studies applying transformers to neuroimaging segmentation problems from 2019 through 2023. The inclusion criteria allow only for peer-reviewed journal papers and conference papers focused on transformer-based segmentation of human brain imaging data. Excluded are the studies dealing with nonneuroimaging data or raw brain signals and electroencephalogram data. Data extraction was performed to identify key study details, including image modalities, datasets, neurological conditions, transformer models, and evaluation metrics. Results were synthesized using a narrative approach. ResultsOf the 1246 publications identified, 67 (5.38%) met the inclusion criteria. Half of all included studies were published in 2022, and more than two-thirds used transformers for segmenting brain tumors. The most common imaging modality was magnetic resonance imaging (n=59, 88.06%), while the most frequently used dataset was brain tumor segmentation dataset (n=39, 58.21%). 3D transformer models (n=42, 62.69%) were more prevalent than their 2D counterparts. The most developed were those of hybrid convolutional neural network-transformer architectures (n=57, 85.07%), where the vision transformer is the most frequently used type of transformer (n=37, 55.22%). The most frequent evaluation metric was the Dice score (n=63, 94.03%). Studies generally reported increased segmentation accuracy and the ability to model both local and global features in brain images. ConclusionsThis review represents the recent increase in the adoption of transformers for neuroimaging segmentation, particularly for brain tumor detection. Currently, hybrid convolutional neural network-transformer architectures achieve state-of-the-art performances on benchmark datasets over standalone models. Nevertheless, their applicability remains highly limited by high computational costs and potential overfitting on small datasets. The heavy reliance of the field on the brain tumor segmentation dataset hints at the use of a more diverse set of datasets to validate the performances of models on a variety of neurological diseases. Further research is needed to define the optimal transformer architectures and training methods for clinical applications. Continuing development may make transformers the state-of-the-art for fast, accurate, and reliable brain magnetic resonance imaging segmentation, which could lead to improved clinical tools for diagnosing and evaluating neurological disorders.https://www.jmir.org/2025/1/e57723 |
| spellingShingle | Maya Iratni Amira Abdullah Mariam Aldhaheri Omar Elharrouss Alaa Abd-alrazaq Zahiriddin Rustamov Nazar Zaki Rafat Damseh Transformers for Neuroimage Segmentation: Scoping Review Journal of Medical Internet Research |
| title | Transformers for Neuroimage Segmentation: Scoping Review |
| title_full | Transformers for Neuroimage Segmentation: Scoping Review |
| title_fullStr | Transformers for Neuroimage Segmentation: Scoping Review |
| title_full_unstemmed | Transformers for Neuroimage Segmentation: Scoping Review |
| title_short | Transformers for Neuroimage Segmentation: Scoping Review |
| title_sort | transformers for neuroimage segmentation scoping review |
| url | https://www.jmir.org/2025/1/e57723 |
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