Analysis of Segment Anything Model (SAM) for Brain Extraction in fMRI studies
Dataset used in the study: Yingying Wang and Hongmi Lee and Brice Kuhl (2023). Ds004590. OpenNeuro. [Dataset] doi: doi:10.18112/openneuro.ds004590.v1.0.0
Overview of Segment Anything Model (SAM) architecture
![Screen Shot 2024-01-08 at 10 11 52 PM](https://private-user-images.githubusercontent.com/11755434/295115811-79735c7d-2573-4a5a-be63-46191eb6b83b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.CZyIJIlh6cu57eP4VVMV8eoaDycHDpugm40sXwFE7WU)
Sample Image from dataset
![Screen Shot 2024-01-08 at 10 12 06 PM](https://private-user-images.githubusercontent.com/11755434/295115929-6d86f206-bc90-4467-9517-da1ec2f281e2.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTYyNDUyMjEsIm5iZiI6MTcxNjI0NDkyMSwicGF0aCI6Ii8xMTc1NTQzNC8yOTUxMTU5MjktNmQ4NmYyMDYtYmM5MC00NDY3LTk1MTctZGExZWMyZjI4MWUyLnBuZz9YLUFtei1BbGdvcml0aG09QVdTNC1ITUFDLVNIQTI1NiZYLUFtei1DcmVkZW50aWFsPUFLSUFWQ09EWUxTQTUzUFFLNFpBJTJGMjAyNDA1MjAlMkZ1cy1lYXN0LTElMkZzMyUyRmF3czRfcmVxdWVzdCZYLUFtei1EYXRlPTIwMjQwNTIwVDIyNDIwMVomWC1BbXotRXhwaXJlcz0zMDAmWC1BbXotU2lnbmF0dXJlPWQwZDM0YWIyZmVkMGNmZTQ2OGRjNWQwZDQ4OTI2MDY1ZTg5MGMzYWE0MWE1MzM2MDZjYTdmZmNiMGE0Y2EwNjImWC1BbXotU2lnbmVkSGVhZGVycz1ob3N0JmFjdG9yX2lkPTAma2V5X2lkPTAmcmVwb19pZD0wIn0.Wh5LpAwfZRVKIsh--tjMbThJs-9vg4jPctJ_EJxmuS8)
![Screen Shot 2024-01-08 at 10 12 22 PM](https://private-user-images.githubusercontent.com/11755434/295115995-e23a7bd0-ab42-42c9-a985-09c2ed228685.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.s7GzoKw62uEGW3IpsovTrb0UeUscbJpU-Eb6_W0kOfA)
![Screen Shot 2024-01-08 at 10 12 32 PM](https://private-user-images.githubusercontent.com/11755434/295116022-f756bbe5-66a6-4c0f-a81b-80099c6a4eb4.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.D0HIb5NsjEcnMOylR09BcftTbHAOwyrcwRvoI8RwPoU)
![Screen Shot 2024-01-08 at 10 12 44 PM](https://private-user-images.githubusercontent.com/11755434/295116055-70707004-6889-4c5b-a819-dbc9b126574b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.LHGmUJN_CaJaPC0KSDp9QMlYBAtJGIFiUbPpkj02sow)
Comparison of results
![Screen Shot 2024-01-08 at 10 13 21 PM](https://private-user-images.githubusercontent.com/11755434/295116203-fc54e4de-1796-46b7-b001-f26b1b44040d.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.Y4wcvW0iej6ywbOBQs902Y9PbSttCGIslr6uFoZXUzg)
[1] Dwith Chenna and Suyash Bhogawar, Segment Anything Model (SAM) For Brain Extraction in fMRI Studies, International Journal of Artificial Intelligence in Medicine (IJAIMED), 1(1), 2023, pp. 1-8. Link: https://iaeme.com/Home/issue/IJAIMED?Volume=1&Issue=1