{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":3662861,"defaultBranch":"master","name":"HCPpipelines","ownerLogin":"Washington-University","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2012-03-08T18:23:25.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1493901?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1715305508.0","currentOid":""},"activityList":{"items":[{"before":"e967a9cdec4d5a6451f2ca7094b93acb5281b52b","after":"097d4c55a4d70c7025acb4836cdebe2bd2c0cd6d","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-31T19:52:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+added two timepoint stages to run MSMSulc.\nAll timepoints at stage 1 in Freesurfer2Caret..sh are processed\nuntil MSMSulc call, at which point processing breaks, and template stage\nbegins. At template stage, all timepoint surfaces are averaged, and\nMSMSulc is run. After template stage, timepoint stage 2 is run that uses\ncommon averaged MSMSulc registered surface.\n+corrected job control in example batch scripts.","shortMessageHtmlLink":"+added two timepoint stages to run MSMSulc."}},{"before":"66953d6591de07f7df3ee6860e5641a063a68102","after":"be7a8c8423950c679d3e45cc1117e1be8072d53b","ref":"refs/heads/master","pushedAt":"2024-05-31T15:17:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"demsarjure","name":"Jure Demsar","path":"/demsarjure","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35776954?s=80&v=4"},"commit":{"message":"Fixed permissions for AnatomicalAverage.sh","shortMessageHtmlLink":"Fixed permissions for AnatomicalAverage.sh"}},{"before":"38888e6a23dd0b9b103a7f6e38f8a7f66888144a","after":"e967a9cdec4d5a6451f2ca7094b93acb5281b52b","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-28T16:35:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+Two-stage mode for longitudinal timepoint processing, to accomodate surface averaging for MSMSulc (which should only run once per all timepoints).","shortMessageHtmlLink":"+Two-stage mode for longitudinal timepoint processing, to accomodate …"}},{"before":"8b59a569f536d2fefdc4acd88b4ce4516ca0576a","after":"38888e6a23dd0b9b103a7f6e38f8a7f66888144a","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-27T21:13:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"fix typos","shortMessageHtmlLink":"fix typos"}},{"before":"2d2f89091e10645ebf69133d3b755c785761d9b6","after":"8b59a569f536d2fefdc4acd88b4ce4516ca0576a","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-26T23:06:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+Have MSMSulc.sh only run in template mode, precluded by surface averaging from all timepoints.\n+Modify argument list in FreeSurfer2Caret.. script to accomodate this.\n+modify longitudinal example batch scripts to wait for jobs to finish where appropriate.","shortMessageHtmlLink":"+Have MSMSulc.sh only run in template mode, precluded by surface aver…"}},{"before":"96541ecc8ad64273bd26d3b49360c779e525a96c","after":"2d2f89091e10645ebf69133d3b755c785761d9b6","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-24T21:45:11.000Z","pushType":"push","commitsCount":33,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master' into feature/longitudinal_fs","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master' into feature/longitudina…"}},{"before":"bced737a8255b698eb57ce61abdddfdeb24253d3","after":"96541ecc8ad64273bd26d3b49360c779e525a96c","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-22T15:44:12.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+batch PostFreesurferPipeline batch script for longitudinal mode","shortMessageHtmlLink":"+batch PostFreesurferPipeline batch script for longitudinal mode"}},{"before":"798c3ed9d83aea4e69588026cdda2476feadec3b","after":"bced737a8255b698eb57ce61abdddfdeb24253d3","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-21T16:47:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+inflatescale argument fix to remove 'developer error'\n+Fix check for T2w image in longitudinal mode.","shortMessageHtmlLink":"+inflatescale argument fix to remove 'developer error'"}},{"before":"d7144fb2375dfb719a3944a04d962064b6d6f40c","after":"798c3ed9d83aea4e69588026cdda2476feadec3b","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-21T15:46:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+fix long-l mode conditions","shortMessageHtmlLink":"+fix long-l mode conditions"}},{"before":"920cd987188065c7f049d197bcfe97ba3445700c","after":"d7144fb2375dfb719a3944a04d962064b6d6f40c","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-20T16:53:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+Added clarification to longitudinal arguments in PostFreeSurfer\n+Proper resolution of longitudinal experiment folder names","shortMessageHtmlLink":"+Added clarification to longitudinal arguments in PostFreeSurfer"}},{"before":null,"after":"4ed77d71a8c00ff604a5be0f058edeff69ba495c","ref":"refs/heads/release-4.8.0","pushedAt":"2024-05-10T01:43:34.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"set RC version","shortMessageHtmlLink":"set RC version"}},{"before":"97184470db277ca3b69b5d4649a71792ac850942","after":"66953d6591de07f7df3ee6860e5641a063a68102","ref":"refs/heads/master","pushedAt":"2024-05-10T01:40:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"recompile RSNRegression matlab for tICAmm mode","shortMessageHtmlLink":"recompile RSNRegression matlab for tICAmm mode"}},{"before":"a64c7eb6d265a02529fd361a2efba299be07a85a","after":"97184470db277ca3b69b5d4649a71792ac850942","ref":"refs/heads/master","pushedAt":"2024-05-10T00:27:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glasserm","name":null,"path":"/glasserm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1517260?s=80&v=4"},"commit":{"message":"Add multiechoCombine.m","shortMessageHtmlLink":"Add multiechoCombine.m"}},{"before":"4aa32949c36b4b75bc97c4810f0af6219367be0f","after":"a64c7eb6d265a02529fd361a2efba299be07a85a","ref":"refs/heads/master","pushedAt":"2024-05-09T21:56:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"sanity check new boolean option, fix spelling","shortMessageHtmlLink":"sanity check new boolean option, fix spelling"}},{"before":"6aea349b621e737e863626f0c2916a12cf372941","after":"4aa32949c36b4b75bc97c4810f0af6219367be0f","ref":"refs/heads/master","pushedAt":"2024-05-09T01:37:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glasserm","name":null,"path":"/glasserm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1517260?s=80&v=4"},"commit":{"message":"*Add option to only run concatination stage of MR+FIX","shortMessageHtmlLink":"*Add option to only run concatination stage of MR+FIX"}},{"before":"7a2da9c3b5c0c8d3381b901f9e6f08085eebd38e","after":"6aea349b621e737e863626f0c2916a12cf372941","ref":"refs/heads/master","pushedAt":"2024-05-08T22:35:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glasserm","name":null,"path":"/glasserm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1517260?s=80&v=4"},"commit":{"message":"add multi-echo support to fMRI","shortMessageHtmlLink":"add multi-echo support to fMRI"}},{"before":"5435d9aaa7dd126e009385fe8d0783308202e235","after":"7a2da9c3b5c0c8d3381b901f9e6f08085eebd38e","ref":"refs/heads/master","pushedAt":"2024-05-06T20:15:58.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Stand Alone MSMSulc.sh script (#290)","shortMessageHtmlLink":"Stand Alone MSMSulc.sh script (#290)"}},{"before":"ea8fdd4a47b9d83838121f3e00dcc7a6d1bc08ff","after":"5435d9aaa7dd126e009385fe8d0783308202e235","ref":"refs/heads/master","pushedAt":"2024-05-03T20:20:01.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Fix isodd check before Pos_b0 exists (#292)","shortMessageHtmlLink":"Fix isodd check before Pos_b0 exists (#292)"}},{"before":null,"after":"4ec0cd15b483fdb7c10d4796cf3274718090466c","ref":"refs/heads/diffusion_oddcheck","pushedAt":"2024-05-02T22:09:26.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"attempt to fix isodd check before Pos_b0 exists","shortMessageHtmlLink":"attempt to fix isodd check before Pos_b0 exists"}},{"before":"ef126fec9a574e13a2f00c0112f2e73f6a85bbc0","after":"ea8fdd4a47b9d83838121f3e00dcc7a6d1bc08ff","ref":"refs/heads/master","pushedAt":"2024-05-01T23:25:54.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Diffusion echo spacing units (#291)\n\nAllows using harmonized time units across pipelines.","shortMessageHtmlLink":"Diffusion echo spacing units (#291)"}},{"before":"95208d04a4efbe7cb9700b58178f06665075084f","after":"920cd987188065c7f049d197bcfe97ba3445700c","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-05-01T21:20:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+this version is tested in batch mode up to PostFreesurfer\n+ppFS pipeline renamed to PostFSLongPrep\n+PostFSLongPrep: fixed an issue with brain mask naming when applying GFC; added more log outputs\n+added FSlong, postFSLongPrep example batch files\n+added SetUpHCPPipeline-long example setup file","shortMessageHtmlLink":"+this version is tested in batch mode up to PostFreesurfer"}},{"before":"1e71908d2b0c9c2cf792672f056200c2e1bce647","after":"814e15cedf47a3b1ef6e2320dd0c17697cab4f23","ref":"refs/heads/diffusion_units","pushedAt":"2024-04-30T03:57:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"update diffusion example to seconds","shortMessageHtmlLink":"update diffusion example to seconds"}},{"before":"338dab587b28ec386e19c93858f7b7fc955b490b","after":"1e71908d2b0c9c2cf792672f056200c2e1bce647","ref":"refs/heads/diffusion_units","pushedAt":"2024-04-30T03:47:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Update DiffusionPreprocessing/DiffPreprocPipeline.sh\n\nCo-authored-by: Michael Harms ","shortMessageHtmlLink":"Update DiffusionPreprocessing/DiffPreprocPipeline.sh"}},{"before":"70c3cce8c4e6400ace9789086bc05b524654c276","after":"170e44b108f9f21b7ec725c15aabdb82c3a2b505","ref":"refs/heads/PR_290","pushedAt":"2024-04-30T01:15:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Update MSMSulc.sh","shortMessageHtmlLink":"Update MSMSulc.sh"}},{"before":"9dbc84d57b9f2f2b7fee14447a82b45ec08260c2","after":"70c3cce8c4e6400ace9789086bc05b524654c276","ref":"refs/heads/PR_290","pushedAt":"2024-04-29T23:56:29.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh","shortMessageHtmlLink":"Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh"}},{"before":null,"after":"338dab587b28ec386e19c93858f7b7fc955b490b","ref":"refs/heads/diffusion_units","pushedAt":"2024-04-29T23:51:06.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"give outer diffusion script a seconds option for echo spacing","shortMessageHtmlLink":"give outer diffusion script a seconds option for echo spacing"}},{"before":"3145a16e288881aab9b0ec57aea596265d86e18c","after":"ef126fec9a574e13a2f00c0112f2e73f6a85bbc0","ref":"refs/heads/master","pushedAt":"2024-04-26T22:14:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"fix excess quotes","shortMessageHtmlLink":"fix excess quotes"}},{"before":"6312b72a4f11c0c44640719afe41db3cd2a0992b","after":"95208d04a4efbe7cb9700b58178f06665075084f","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-04-26T20:46:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"PostFreeSurferPipeline.sh:\n+longitudinal mode, template and timepoint options are needed to correctly resolve timepoint/template directory names.\nPrePostFreeSurferPipeline-long.sh:\n+brain mask in native space is computed as maximum of FS timepoint masks\n+acpc_dc template images are computed as average of corresponding timepoint images\n+timepoint and template FS-based brainmasks are saved with _orig suffix\n+single brain mask for all timepoints\n+brain mask in MNI space is applied to resampled images","shortMessageHtmlLink":"PostFreeSurferPipeline.sh:"}},{"before":null,"after":"9dbc84d57b9f2f2b7fee14447a82b45ec08260c2","ref":"refs/heads/PR_290","pushedAt":"2024-04-26T02:54:01.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"coalsont","name":"Tim Coalson","path":"/coalsont","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1513170?s=80&v=4"},"commit":{"message":"Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh","shortMessageHtmlLink":"Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh"}},{"before":"0898ae019f8b618245413af088575c0318c183a3","after":"6312b72a4f11c0c44640719afe41db3cd2a0992b","ref":"refs/heads/feature/longitudinal_fs","pushedAt":"2024-04-25T19:51:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mmilch01","name":null,"path":"/mmilch01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6777679?s=80&v=4"},"commit":{"message":"+copy acpc_dc_restore to acpc_dc\n+Fix T2w detection in CreateMyelinMaps in longitudinal case\n+GeneralScheme.puml update","shortMessageHtmlLink":"+copy acpc_dc_restore to acpc_dc"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEWVpzeQA","startCursor":null,"endCursor":null}},"title":"Activity · Washington-University/HCPpipelines"}