{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":392297962,"defaultBranch":"stable","name":"FastSurfer","ownerLogin":"dkuegler","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2021-08-03T11:45:14.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/12848082?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1714764192.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"a000faa1a5b9fd2355b6d9e8502c64929dd0ae07","ref":"refs/heads/fix/518-model-download-issue","pushedAt":"2024-05-03T19:23:12.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"add dockerhub deployment workflow (#278) (#417)\n\nCo-authored-by: Andreas Girodi <87191977+agirodi@users.noreply.github.com>","shortMessageHtmlLink":"add dockerhub deployment workflow (Deep-MI#278) (Deep-MI#417)"}},{"before":"d096571a659ecd850deeafbcf1a09f4140defeba","after":"4faacf45f8b54211039f052eba5131c63dcb9e49","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-30T10:03:28.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- fix parts of the sphinx resolve of links\n- suppress autosectionlabel warnings in sphinx\n- fix doc\n\nrecon-surf\n- fix the vox-size check\n- fix which stats are calculated when\n\nrun_fastsurfer.sh\n- remove echo_quoted","shortMessageHtmlLink":"- fix parts of the sphinx resolve of links"}},{"before":"92c48dd00075e7077b9e2ba79de9d88a766d16a9","after":null,"ref":"refs/heads/fix/cmd-interface","pushedAt":"2024-04-23T09:12:44.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"b6060eea16f405695b2cda6cf31add8cee2c02bb","after":"d096571a659ecd850deeafbcf1a09f4140defeba","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-21T08:45:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Update run_fastsurfer.sh","shortMessageHtmlLink":"Update run_fastsurfer.sh"}},{"before":"88854f23a1b3c214d6cfbd23aef4d89cb923dbab","after":"b6060eea16f405695b2cda6cf31add8cee2c02bb","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-20T14:19:50.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- fix FreeSurfer license parameter assignment\n- remove nbsphinx from sphinx extensions","shortMessageHtmlLink":"- fix FreeSurfer license parameter assignment"}},{"before":"38be0089d4a34c38d84f5386c7a61dd587296fbf","after":null,"ref":"refs/heads/fix/reconsurf-softlink","pushedAt":"2024-04-20T12:03:26.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"95a559d94e6b8c06e2c91164afd3d442ca2cdcfc","after":null,"ref":"refs/heads/fix/conform","pushedAt":"2024-04-20T11:50:22.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"b572bae16fe14b5b2509d992db68397db187b3ef","after":null,"ref":"refs/heads/feature/hypvinn","pushedAt":"2024-04-20T11:43:46.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"907c5a81179a56b1e2ffe89d2e71d09aea638404","after":null,"ref":"refs/heads/feature/hypvinn-rebased","pushedAt":"2024-04-20T11:43:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":null,"after":"b572bae16fe14b5b2509d992db68397db187b3ef","ref":"refs/heads/feature/hypvinn","pushedAt":"2024-04-19T17:53:12.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fixes to the commandline etc","shortMessageHtmlLink":"Fixes to the commandline etc"}},{"before":null,"after":"92c48dd00075e7077b9e2ba79de9d88a766d16a9","ref":"refs/heads/fix/cmd-interface","pushedAt":"2024-04-19T17:34:17.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fix bugs introduced by #501.\n\nCerebNet/utils/load_config.py\n- remove unused setup_options\n- fix typing of yacs.config\n- fix assignment of cfg.LOG_DIR which cannot be a Path, but must be a string (yacs requirement)\n\nCerebNet/run_prediction.py\n- fix the path to the checkpoint_paths.yaml file\n- clean up the imports\n\nFastSurferCNN/utils/parser_defaults.py\n- remove unwanted commas, they make the value a tuple\n\nFastSurferCNN/run_prediction.py\n- Fix parameter names in main function\n- add a try-except block in main\n- add/fix typing\n- fix typo in main\n\nrecon_surf/N4_bias_correct.py\n- Formatting (e.g. constants are UPPERCASE)\n- fix typos\n- fix incorrect conversion of default \"do nothing strings\" to Path\n\ndoc/overview/OUTPUT_FILES.md\n- fix the formatting of the tables","shortMessageHtmlLink":"Fix bugs introduced by Deep-MI#501."}},{"before":"013d91ec3c10877363ae52d1b079daddbb1d04ca","after":"88854f23a1b3c214d6cfbd23aef4d89cb923dbab","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-17T15:40:43.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"add --segstats_legacy flag to run_fastsurfer.sh","shortMessageHtmlLink":"add --segstats_legacy flag to run_fastsurfer.sh"}},{"before":"7c5e709ac703f62e6b85be8751a5815e1c5060af","after":null,"ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-17T15:38:23.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"7344e80646ba9ca9af9ec7f177cf973502e88d4b","after":"013d91ec3c10877363ae52d1b079daddbb1d04ca","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-17T15:33:29.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"add --segstats_legacy flag to run_fastsurfer.sh","shortMessageHtmlLink":"add --segstats_legacy flag to run_fastsurfer.sh"}},{"before":"92587c92ae0889e62ea5d2b14dd5b23029472170","after":"7344e80646ba9ca9af9ec7f177cf973502e88d4b","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-17T14:55:24.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"add --segstats_legacy flag to run_fastsurfer.sh","shortMessageHtmlLink":"add --segstats_legacy flag to run_fastsurfer.sh"}},{"before":"67304c59c3283638978ed3fc60fb65551c159a0a","after":"92587c92ae0889e62ea5d2b14dd5b23029472170","ref":"refs/heads/feature/segstats/brainvolstats","pushedAt":"2024-04-17T14:24:26.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"fix vox_vol multiplication in PVMeasure\nbetter save_maps test","shortMessageHtmlLink":"fix vox_vol multiplication in PVMeasure"}},{"before":"8665af42bdf9bce9c7857a01a7b9845b0d3bf5d3","after":"7c5e709ac703f62e6b85be8751a5815e1c5060af","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-17T13:59:17.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- fix the relative paths","shortMessageHtmlLink":"- fix the relative paths"}},{"before":"489107fb319460831ffcd1da94a95e25ed3db670","after":"8665af42bdf9bce9c7857a01a7b9845b0d3bf5d3","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-15T08:58:02.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- fix the relative paths","shortMessageHtmlLink":"- fix the relative paths"}},{"before":"ba6e2fb074642979d9466997613155f424244288","after":"489107fb319460831ffcd1da94a95e25ed3db670","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-12T16:59:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Apply suggestions from code review\r\n\r\n- quick fix the relative paths","shortMessageHtmlLink":"Apply suggestions from code review"}},{"before":"f138bce961fa5b018b842b54f546a8e7ae3ac66f","after":"ba6e2fb074642979d9466997613155f424244288","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-12T16:37:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- fix build in different directory","shortMessageHtmlLink":"- fix build in different directory"}},{"before":"8e4a4c196bbb8bc5393b1deb5da46519e16abc91","after":null,"ref":"refs/heads/feature/build-singularity","pushedAt":"2024-04-12T15:38:41.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"}},{"before":"eb0104a40264a13b5e60d02a48c84c0e4fe811d7","after":"f138bce961fa5b018b842b54f546a8e7ae3ac66f","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-12T15:35:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- switch sphinx-argparse option to module, because filename depends on the current working directory\n- fix
in segstats epilog","shortMessageHtmlLink":"- switch sphinx-argparse option to module, because filename depends o…"}},{"before":"77c12ae2cf2032770e11b044111b86d10673af7e","after":"eb0104a40264a13b5e60d02a48c84c0e4fe811d7","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-12T15:06:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"- remove/replace multi-level inclusion of doc (e.g. remove doc/START.md => doc/index.rst, remodel doc/overview/intro to rst)\n- add license to documentation\n- add doc for cerebnet, recon_surf and fastsurfercnn folders (and scripts)\n- fix heading levels and links in recon_surf/README.md\n- fix test message\n- add and configure argparse extension for sphinx, so argparse argument help text etc is properly included\n- complete the custom sphinx extension fix_links, which rewrites links so they map to the correct place in the documentation\n- configure the fix_links extension\n- add program-output extension to include help messages of batch scripts\n- add FastSurferCNN/(run_model,run_prediction,generate_hdf5,segstats).py to the scripts doc directory (self-documenting)\n- change the call interface of run_prediction, so it uses a main function\n- add dataclass for subject_directory parameters and migrate help text for those parameters into the dataclass, so it can be used in multiple places\n- some smaller argument fixes in run_model, train, models.optimizers\n- remove extra text from LICENSE","shortMessageHtmlLink":"- remove/replace multi-level inclusion of doc (e.g. remove doc/START.…"}},{"before":null,"after":"95a559d94e6b8c06e2c91164afd3d442ca2cdcfc","ref":"refs/heads/fix/conform","pushedAt":"2024-04-08T21:36:51.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fix getscale for f_low != 0 (default value)\n\n- As reported in #505, getscale unexpectedly corrupts src_max (via src_min), if f_low is not 0.0 (the default value).\n- Updated variable names, formatting, comments\n- Optimized double calls to min and max (explicitly getscale and implicitly via np.histogram).","shortMessageHtmlLink":"Fix getscale for f_low != 0 (default value)"}},{"before":"2239ab1b8bd39a6eea4418a6b52cc32233ebd162","after":"77c12ae2cf2032770e11b044111b86d10673af7e","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-05T15:29:05.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"changing docker and singularity links back to relative links","shortMessageHtmlLink":"changing docker and singularity links back to relative links"}},{"before":"278d2e492e1b0161c39883845acc16b7dbcc18a7","after":"2239ab1b8bd39a6eea4418a6b52cc32233ebd162","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-05T12:56:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Links now point to source code of object on GitHub\n\n- replacing hardcoded 'stable' branch with 'dev'","shortMessageHtmlLink":"Links now point to source code of object on GitHub"}},{"before":"ddbe1cf38fad461316ab15273ef467441a41873f","after":"278d2e492e1b0161c39883845acc16b7dbcc18a7","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-05T12:30:39.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fixes to the sphinx doc\n\n- Rename API pages (remove API and References)\n- Add warning to toplevel API doc -- in development\n- Reorder/sort overview and API docs\n- move folder images to doc\n- Add/remove duplicate documents and instead include the main document\n - Docker.md\n - Singularity.md\n - README.md: One README file is re-used in doc in multiple places by adding anchors and \"include\" blocks in doc/START.md and doc/overview/INTRO.md\n - doc/overview/README.md\n - doc/index.rst\n - doc/START.md\n - doc/overview/index.rst\n - doc/overview/INTRO.md\n- add sphinx extension to rewrite links\n- add doc to dockerignore\n- update sphinx configuration\n- some fixes to sphinx doc","shortMessageHtmlLink":"Fixes to the sphinx doc"}},{"before":"6634302b7c589f7e8c9dd142ce5d328364ce398a","after":"ddbe1cf38fad461316ab15273ef467441a41873f","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-04T16:57:40.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fixes to the sphinx doc\n\n- Rename API pages (remove API and References)\n- Add warning to toplevel API doc -- in development\n- Reorder/sort overview and API docs\n- move folder images to doc\n- Add/remove duplicate documents and instead include the main document\n - Docker.md\n - Singularity.md\n - README.md: One README file is re-used in doc in multiple places by adding anchors and \"include\" blocks in doc/START.md and doc/overview/INTRO.md\n - doc/overview/README.md\n - doc/index.rst\n - doc/START.md\n - doc/overview/index.rst\n - doc/overview/INTRO.md\n- add sphinx extension to rewrite links\n- add doc to dockerignore\n- update sphinx configuration\n- some fixes to sphinx doc","shortMessageHtmlLink":"Fixes to the sphinx doc"}},{"before":null,"after":"6634302b7c589f7e8c9dd142ce5d328364ce398a","ref":"refs/heads/feature/sphinx-links","pushedAt":"2024-04-04T09:37:22.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Fixes to the sphinx doc\n\n- Rename API pages (remove API and References)\n- Add warning to toplevel API doc -- in development\n- Reorder/sort overview and API docs\n- move folder images to doc\n- Add/remove duplicate documents and instead include the main document\n - Docker.md\n - Singularity.md\n - README.md: One README file is re-used in doc in multiple places by adding anchors and \"include\" blocks in doc/START.md and doc/overview/INTRO.md\n - doc/overview/README.md\n - doc/index.rst\n - doc/START.md\n - doc/overview/index.rst\n - doc/overview/INTRO.md\n- add sphinx extension to rewrite links\n- add doc to dockerignore\n- update sphinx configuration\n- some fixes to sphinx doc","shortMessageHtmlLink":"Fixes to the sphinx doc"}},{"before":"bb2540b8ad0c2eef757aadfa684dce723108743f","after":"8e4a4c196bbb8bc5393b1deb5da46519e16abc91","ref":"refs/heads/feature/build-singularity","pushedAt":"2024-04-04T09:36:16.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"dkuegler","name":"David Kügler","path":"/dkuegler","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12848082?s=80&v=4"},"commit":{"message":"Add build/conversion to Singularity as an option to the Docker/build.py script\n\n- Also update and clean up the docs.\n- Fix a typo in Dockerfile.\n- Fix some formatting.\n- Add Docker and Singularity READMEs to the sphinx doc.","shortMessageHtmlLink":"Add build/conversion to Singularity as an option to the Docker/build.…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEQQ2XSgA","startCursor":null,"endCursor":null}},"title":"Activity · dkuegler/FastSurfer"}