{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":361768356,"defaultBranch":"main","name":"model_seg_sci","ownerLogin":"ivadomed","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-04-26T13:52:55.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/67157284?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726845657.0","currentOid":""},"activityList":{"items":[{"before":"1f647a6c31025d2049f4322c006af3ee0c87dddc","after":"813caae549a6eb4bfd69b392ee53129f304e6a9e","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-21T12:41:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Generate sagittal lesion QC report","shortMessageHtmlLink":"Generate sagittal lesion QC report"}},{"before":"8d9b7b992f006b85a183d519974f729eabd33aaf","after":"1f647a6c31025d2049f4322c006af3ee0c87dddc","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-20T17:36:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add README for the midsagittal lesion length and width analysis","shortMessageHtmlLink":"Add README for the midsagittal lesion length and width analysis"}},{"before":"6a06f868e7ed6ea4aa0ded1f95e7804d93f046bd","after":"8d9b7b992f006b85a183d519974f729eabd33aaf","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-20T16:44:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Use '-largest 1' to keep only the largest connected component. Context: https://github.com/ivadomed/model_seg_sci/pull/96\\#issuecomment-2364121461","shortMessageHtmlLink":"Use '-largest 1' to keep only the largest connected component. Context: "}},{"before":"02e93215cfdfc6450bfa709e9a5c1cc2451f5996","after":"6a06f868e7ed6ea4aa0ded1f95e7804d93f046bd","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-20T15:49:11.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Remove 'CUDA_VISIBLE_DEVICES=1 SCT_USE_GPU=1' for the contrast-agnostic model for now\n\nContext: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4633","shortMessageHtmlLink":"Remove 'CUDA_VISIBLE_DEVICES=1 SCT_USE_GPU=1' for the contrast-agnost…"}},{"before":"426b718ddc9a417ad4675be16d6e45227c080f6e","after":"02e93215cfdfc6450bfa709e9a5c1cc2451f5996","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-20T15:37:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Change logic how to save XLS files produced by sct_analyze_lesion. If we use '-ofolder' for sct_analyze_lesion, then QC report fails.","shortMessageHtmlLink":"Change logic how to save XLS files produced by sct_analyze_lesion. If…"}},{"before":null,"after":"426b718ddc9a417ad4675be16d6e45227c080f6e","ref":"refs/heads/jv/ismrm_2025-midsagittal_lesion_length_and_width","pushedAt":"2024-09-20T15:20:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add script to segment the spinal cord and lesions from T2w images and compute the midsagittal lesion length and width.","shortMessageHtmlLink":"Add script to segment the spinal cord and lesions from T2w images and…"}},{"before":"6079aac23f69fb5b7dae6464cff12062d495c569","after":"e18fb4838c032c87cc0f4c2116303ac2f41380d8","ref":"refs/heads/main","pushedAt":"2024-09-20T14:35:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add lesion-analysis tutorial","shortMessageHtmlLink":"Add lesion-analysis tutorial"}},{"before":"725280eb496eabe17b50915767a6d16b8cfe5450","after":"6079aac23f69fb5b7dae6464cff12062d495c569","ref":"refs/heads/main","pushedAt":"2024-09-20T12:35:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Remove https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4489 as it is now part of SCT v6.4","shortMessageHtmlLink":"Remove spinalcordtoolbox/spinalcordtoolbox#4489 as it is now part of …"}},{"before":"e8bfb8366b89ec715061eaa26ac70963171e8f1c","after":"725280eb496eabe17b50915767a6d16b8cfe5450","ref":"refs/heads/main","pushedAt":"2024-09-20T12:17:03.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Drop 'seed' column as it does not make sense after .groupby().mean()","shortMessageHtmlLink":"Drop 'seed' column as it does not make sense after .groupby().mean()"}},{"before":"a719d16d32e1566a6e14bef9738f0201b0c179d7","after":"e8bfb8366b89ec715061eaa26ac70963171e8f1c","ref":"refs/heads/main","pushedAt":"2024-09-16T09:18:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"naga-karthik","name":"Naga Karthik Enamundram","path":"/naga-karthik","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/53445351?s=80&v=4"},"commit":{"message":"temporary updates to regenerate figure for poster","shortMessageHtmlLink":"temporary updates to regenerate figure for poster"}},{"before":"4a596311aa58d8e8be091197ccdf18e719cc7641","after":"33e652e84d2cbb76b05269519925b9f940068872","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-09-06T21:55:55.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add BIDS to nnUNet conversion script for 3-class labels (cord, edema, hemorrhage)","shortMessageHtmlLink":"Add BIDS to nnUNet conversion script for 3-class labels (cord, edema,…"}},{"before":"35c06681beb841e3e8fae5562a228590b907a517","after":"4a596311aa58d8e8be091197ccdf18e719cc7641","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-09-06T11:14:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Update available_trainers","shortMessageHtmlLink":"Update available_trainers"}},{"before":"799e6c682efa4ab79f28e2db17d11978a6e7fdfc","after":"35c06681beb841e3e8fae5562a228590b907a517","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-09-03T18:40:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Create a separate function to create the dataset.json file","shortMessageHtmlLink":"Create a separate function to create the dataset.json file"}},{"before":"8c9c1b57318b5a97af166192ff7a32722cc47b18","after":"f00647ce6b99c5a54b19e50d67c866611155f738","ref":"refs/heads/jv/run_inference_site_003_and_site_012","pushedAt":"2024-08-29T18:17:24.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"exit 1 --> exit 0","shortMessageHtmlLink":"exit 1 --> exit 0"}},{"before":"fd56e83744fb98816b6c068350ede476a47ca6ec","after":"8c9c1b57318b5a97af166192ff7a32722cc47b18","ref":"refs/heads/jv/run_inference_site_003_and_site_012","pushedAt":"2024-08-29T17:30:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"fix grep syntax to be MacOS compatible","shortMessageHtmlLink":"fix grep syntax to be MacOS compatible"}},{"before":"7627d2714135ac7317c137dcf07dd111c5b23422","after":"fd56e83744fb98816b6c068350ede476a47ca6ec","ref":"refs/heads/jv/run_inference_site_003_and_site_012","pushedAt":"2024-08-29T17:24:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"remove accidentally inserted line","shortMessageHtmlLink":"remove accidentally inserted line"}},{"before":"d58dd866c4ba2e32ce6c72f83d79918b08a4ec33","after":"7627d2714135ac7317c137dcf07dd111c5b23422","ref":"refs/heads/jv/run_inference_site_003_and_site_012","pushedAt":"2024-08-29T17:22:16.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Include 'acq-sag'","shortMessageHtmlLink":"Include 'acq-sag'"}},{"before":"a73989857b6c4c51ebe3e8c24dd4316e23b9357e","after":"d58dd866c4ba2e32ce6c72f83d79918b08a4ec33","ref":"refs/heads/jv/run_inference_site_003_and_site_012","pushedAt":"2024-08-29T16:11:37.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Improve comment, add echo","shortMessageHtmlLink":"Improve comment, add echo"}},{"before":"26ffbd1616af2d8babc6d1839a63d854387066cb","after":"a719d16d32e1566a6e14bef9738f0201b0c179d7","ref":"refs/heads/main","pushedAt":"2024-08-29T14:58:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Print also unformatted p-value","shortMessageHtmlLink":"Print also unformatted p-value"}},{"before":null,"after":"12fce0ae4afda1a782439ce9b6838b62e445780a","ref":"refs/heads/jv/remove_generate_new_lesions_folder","pushedAt":"2024-08-29T14:51:25.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Delete generate_new_lesions folder","shortMessageHtmlLink":"Delete generate_new_lesions folder"}},{"before":"09ff781ace9c78acc60b21886327f724a05283d8","after":"799e6c682efa4ab79f28e2db17d11978a6e7fdfc","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-29T14:50:10.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add cropping option to crop around the lesion","shortMessageHtmlLink":"Add cropping option to crop around the lesion"}},{"before":"9f2573407d2863387fa320224822a1b4726d98e2","after":"409dcabc38fd6a08ca3e26fbab0edc29f42b687c","ref":"refs/heads/jv/run_inference_on_spine-generic","pushedAt":"2024-08-28T11:20:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add ref to SCT v6.4","shortMessageHtmlLink":"Add ref to SCT v6.4"}},{"before":"b3ae7a778f2ecee24ec5947398caf1d2399de462","after":"09ff781ace9c78acc60b21886327f724a05283d8","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T22:52:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"fix typo in path","shortMessageHtmlLink":"fix typo in path"}},{"before":"448fa5af0b03250e94db8a43c447dfbeaf91d7fb","after":"b3ae7a778f2ecee24ec5947398caf1d2399de462","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T22:50:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add details about venv; remove conda commands\n\n- as MetricsReloaded is part of the nnunet conda venv, there is no need for these commands","shortMessageHtmlLink":"Add details about venv; remove conda commands"}},{"before":"f1968de9b3d1bc1b6668297161b006eb773ebdb5","after":"448fa5af0b03250e94db8a43c447dfbeaf91d7fb","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T22:42:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Check whether the dataset is already preprocessed, if so, skip preprocessing","shortMessageHtmlLink":"Check whether the dataset is already preprocessed, if so, skip prepro…"}},{"before":"3923fedc8a1d585dc0a70abcc716e588344849e6","after":"f1968de9b3d1bc1b6668297161b006eb773ebdb5","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T22:36:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add testing","shortMessageHtmlLink":"Add testing"}},{"before":"a2ef13cae7d81fe71a820a7df5b813d0c1503fcf","after":"3923fedc8a1d585dc0a70abcc716e588344849e6","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T18:30:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"update example dataset number","shortMessageHtmlLink":"update example dataset number"}},{"before":null,"after":"a2ef13cae7d81fe71a820a7df5b813d0c1503fcf","ref":"refs/heads/jv/segment_hemorrhage","pushedAt":"2024-08-27T18:23:51.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add script to run nnUNet workflow","shortMessageHtmlLink":"Add script to run nnUNet workflow"}},{"before":"26f7fb5cb345fd9641bda0c988513e1e2e206858","after":"9f2573407d2863387fa320224822a1b4726d98e2","ref":"refs/heads/jv/run_inference_on_spine-generic","pushedAt":"2024-08-26T20:11:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add missing 'SCT_USE_GPU=1'","shortMessageHtmlLink":"Add missing 'SCT_USE_GPU=1'"}},{"before":null,"after":"26f7fb5cb345fd9641bda0c988513e1e2e206858","ref":"refs/heads/jv/run_inference_on_spine-generic","pushedAt":"2024-08-26T19:58:19.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"valosekj","name":"Jan Valosek","path":"/valosekj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/39456460?s=80&v=4"},"commit":{"message":"Add script to run SCIsegV2 inference on the spine-generic multi-subject dataset","shortMessageHtmlLink":"Add script to run SCIsegV2 inference on the spine-generic multi-subje…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMVQxMjo0MToxMy4wMDAwMDBazwAAAAS8s1Ld","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMVQxMjo0MToxMy4wMDAwMDBazwAAAAS8s1Ld","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0yNlQxOTo1ODoxOS4wMDAwMDBazwAAAASko3In"}},"title":"Activity · ivadomed/model_seg_sci"}