{"id":15290457,"url":"https://github.com/abysslover/deepparcellation","last_synced_at":"2025-04-13T10:12:09.545Z","repository":{"id":62567488,"uuid":"387636147","full_name":"abysslover/deepparcellation","owner":"abysslover","description":"DeepParcellation: deep learning for robust brain MRI parcellation of elderly East Asians","archived":false,"fork":false,"pushed_at":"2022-12-12T05:16:35.000Z","size":101,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-13T10:12:06.678Z","etag":null,"topics":["brain","mri","parcellation-model"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/abysslover.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-07-20T01:19:58.000Z","updated_at":"2024-12-27T10:17:06.000Z","dependencies_parsed_at":"2023-01-27T14:01:04.787Z","dependency_job_id":null,"html_url":"https://github.com/abysslover/deepparcellation","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abysslover%2Fdeepparcellation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abysslover%2Fdeepparcellation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abysslover%2Fdeepparcellation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abysslover%2Fdeepparcellation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/abysslover","download_url":"https://codeload.github.com/abysslover/deepparcellation/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248695481,"owners_count":21146956,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["brain","mri","parcellation-model"],"created_at":"2024-09-30T16:08:15.829Z","updated_at":"2025-04-13T10:12:09.527Z","avatar_url":"https://github.com/abysslover.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DeepParcellation Package\nDeepParcellation: deep learning for robust brain MRI parcellation of elderly East Asians\n\n### Contributions\n- The project was initiated by Dr. Lim (abysslover) and Dr. Choi (yooha1003).\n- The code is written by Dr. Lim at Gwangju Alzheimer's \u0026 Related Dementia (GARD) Cohort Research Center ([GARD CRC](http://nrcd.re.kr/)), Chosun University.\n- This research was conducted in collaborations with the following people:\nEun-Cheon Lim\u003csup\u003e1\u003c/sup\u003e, Uk-Su Choi\u003csup\u003e1\u003c/sup\u003e, Kyu Yeong Choi\u003csup\u003e1\u003c/sup\u003e, Jang Jae Lee\u003csup\u003e1\u003c/sup\u003e, Yul-Wan Sung\u003csup\u003e2\u003c/sup\u003e, Seji Ogawa\u003csup\u003e2\u003c/sup\u003e, Byeong-Chae Kim\u003csup\u003e3\u003c/sup\u003e Kun Ho Lee\u003csup\u003e1\u003c/sup\u003e and Jungsoo Gim\u003csup\u003e1\u003c/sup\u003e.\n\n1. Gwangju Alzheimer's \u0026 Related Dementia (GARD) Cohort Research Center, Chosun University, Gwangju, 61452, Republic of Korea\n2. Kansei Fukushi Research Institute, Tohoku Fukushi University, Sendai, Miyagi, 9893201, Japan\n3. Department of Neurology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea\n\n- The manuscript is available in the [Frontiers in Aging Neuroscience](https://www.frontiersin.org/articles/10.3389/fnagi.2022.1027857/full).\n\n## Getting Started\nA step-by-step tutorial is provided in the following sections.\n\n### Prerequisites\nYou should install CUDA-enabled GPU cards with at least 8GB GPU memory manufactured by nVidia, e.g., Titan XP.\n\n### Prepare T1-weighted MR images\n\n1. Convert MR images to Neuroimaging Informatics Technology Initiative (NIfTI) format.\n2. The parent directory name of a NIfTI file path will be used as **Subject Id** during prediction.\n3. You can specify either **an input path** of the NIfTI file or **input direcotry** of many NIfTI files.\n\n### Install DeepParcellation\n1. Install Anaconda\n   - Download an Anaconda distribution: [Link](https://www.anaconda.com/distribution/)\n2. Create a Conda environment\n```\n\tconda create -n deepparc python=3.8 -y\n```\n3. Install DeepParcellation (CPU mode)\n```\n\tconda activate deepparc\n\tpip install deepparcellation\n```\n\n4. Install DeepParcellation (GPU mode)\n```\n\tconda activate deepparc\n\tpip install deepparcellation\n\tconda install cudnn=7.6.5 -c anaconda -y\n\tconda install cudatoolkit=10.1.243 -c conda-forge -y\n\tpip uninstall tensorflow -y\n\tpip install tensorflow-gpu==2.2.0\n\tpip uninstall keras -y\n\tconda install keras-gpu=2.4.3 -c anaconda -y\n```\n5. Install DeepParcellation (Mac with M1 Chip)\n```\n\tconda activate deepparc\n\texport GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=1\n\texport GRPC_PYTHON_BUILD_SYSTEM_ZLIB=1\n\texport CFLAGS=\"-I/opt/homebrew/opt/openssl/include\"\n\texport LDFLAGS=\"-L/opt/homebrew/opt/openssl/lib\"\n\tconda install -c apple tensorflow-deps -y\n\tpip install tensorflow-macos\n\tpip install deepparcellation\n```\n6. Run DeepParcellation\n```\n\tconda activate deepparc\n\tdeepparcellation -o=/tmp/test --i=./subject-0-0000/test.nii.gz\n\tor\n\tdeepparcellation -o=/tmp/test --i=./\n```\n**NOTE**:\n1. You must always **activate the conda enviroment** before running DeepParcellation if you opened a **new console**.\n\n### Contact\nPlease contact abysslover@gmail.com if you have any questions about DeepParcellation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabysslover%2Fdeepparcellation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabysslover%2Fdeepparcellation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabysslover%2Fdeepparcellation/lists"}