{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":741737744,"defaultBranch":"master","name":"fmriprep","ownerLogin":"NingAnMe","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2024-01-11T02:17:44.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/13708622?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1704955486.0","currentOid":""},"activityList":{"items":[{"before":"de72651338ee7c98107d3987c7130eea09616e64","after":"f3e95d9c88a5889baa61b34dceb9b10934b5f6f9","ref":"refs/heads/master","pushedAt":"2024-02-05T13:22:42.000Z","pushType":"push","commitsCount":55,"pusher":{"login":"NingAnMe","name":"Ning An","path":"/NingAnMe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13708622?s=80&v=4"},"commit":{"message":"ENH: separate anatomical and functional reports per session for densely sampled dataset (#3191)\n\nenh: beyond a certain number of session for a single subject (4), we\r\nseparate the anatomical report from the functional and we separate the\r\nfunctional reports per session. For fewer sessions than 4, we keep the\r\noriginal behavior of aggregating all sessions and the anatomical in one\r\nreport.\r\n\r\nenh: find the suitable bootstrapfile within generate_reports rather than\r\nbefore\r\n\r\nenh: add session_list argument to generate_reports\r\n\r\nBuilds on top of #3177\r\n\r\nCloses #3080\r\n\r\n---------\r\n\r\nCo-authored-by: Oscar Esteban <code@oscaresteban.es>\r\nCo-authored-by: Chris Markiewicz <markiewicz@stanford.edu>","shortMessageHtmlLink":"ENH: separate anatomical and functional reports per session for dense…"}},{"before":"1d0bbcf759d7fce7f1326bbe7e690ae496d399cb","after":"a91162a3d3dee4e96a5db742776a7dc8c2795c4f","ref":"refs/heads/deepprep","pushedAt":"2024-01-12T09:01:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NingAnMe","name":"Ning An","path":"/NingAnMe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13708622?s=80&v=4"},"commit":{"message":"FIX: fix the None bug","shortMessageHtmlLink":"FIX: fix the None bug"}},{"before":"a84f45205914829ba776e9f584aa52fcd31321a2","after":"1d0bbcf759d7fce7f1326bbe7e690ae496d399cb","ref":"refs/heads/deepprep","pushedAt":"2024-01-12T01:44:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NingAnMe","name":"Ning An","path":"/NingAnMe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13708622?s=80&v=4"},"commit":{"message":"NEW: add filedmap workflow","shortMessageHtmlLink":"NEW: add filedmap workflow"}},{"before":"bfa25c35a90b42e5e71c40011073992ec2ddb023","after":"a84f45205914829ba776e9f584aa52fcd31321a2","ref":"refs/heads/deepprep","pushedAt":"2024-01-11T09:40:02.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"NingAnMe","name":"Ning An","path":"/NingAnMe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13708622?s=80&v=4"},"commit":{"message":"Merge tag '23.2.0' into deepprep\n\n23.2.0 (January 10, 2024)\n\nNew feature release in the 23.2.x series.\n\nThis release wraps up a significant refactor of fMRIPrep. The main new features\ncan be used with the ``--level`` and ``--derivatives`` flags.\n\nThe ``--level`` flag can take the arguments ``minimal``, ``resampling`` or\n``full``. The default is ``full``, which should produce nearly the same results\nas previous versions. ``minimal`` will produce only the minimum necessary to\ndeterministically generate the remaining derivatives. ``resampling`` will produce\nsome additional derivatives, intended to simplify resampling with other tools.\n\nThe ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``,\nfor example ``--derivatives anat=$SMRIPREP_DIR``.  If provided, fMRIPrep will\nread the specified directories for pre-computed derivatives. If a derivative is\nfound, it will be used instead of computing it from scratch. If a derivative is\nnot found, fMRIPrep will compute it and proceed as usual.\n\nTaken together, these features can allow a dataset provider to run a minimal\nfMRIPrep run, targeting many output spaces, while a user can then run a\n``--derivatives`` run to generate additional derivatives in only the output\nspaces they need. Another use case is to provide an precomputed derivative\nto override the default fMRIPrep behavior, enabling easier workarounds for\nbugs or experimentation with alternatives.\n\nAdditionally, this release includes a number of bug fixes and improvements.\nThis release adds support for MSM-Sulc, improving the alignment of subject\nsurfaces to the fsLR template. This process is enabled by default, but may\nbe disabled with the ``--no-msm`` flag.\n\nThis release resolves a number of issues with fieldmaps inducing distortions\nduring correction. Phase difference and direct fieldmaps are now masked correctly,\npreventing the overestimation of distortions outside the brain. Additionally,\nwe now implement Jacobian weighting during unwarping, which corrects for compression\nand expansion effects on signal intensity. To disable Jacobian weighting, use\n``--ignore fmap-jacobian``.\n\nFinally, a new resampling method has been added, to better account for\nsusceptibility distortion and motion in a single shot resampling to a volumetric\ntarget space. We anticipate extending this to surface targets in the future.\n\n* FIX: Restore --ignore sbref functionality (#3180)\n* FIX: Retrieve atlas ROIs at requested density (#3179)\n* FIX: Keep minctracc executable in FreeSurfer installation (#3175)\n* FIX: Exclude echo entity from optimally combined derivatives (#3166)\n* FIX: Disable boldref-space outputs unless requested (#3159)\n* FIX: Tag memory estimates in resamplers (#3150)\n* FIX: Final revisions for next branch (#3134)\n* FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098)\n* FIX: Connect EPI-to-fieldmap transform (#3099)\n* FIX: Use Py2-compatible version file template for fmriprep-docker (#3101)\n* FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077)\n* ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (#3186)\n* ENH: Exclude non-steady-state volumes from confound correlation plot (#3171)\n* ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (#3146)\n* ENH: Restore carpetplot and other final adjustments (#3131)\n* ENH: Restore CIFTI-2 generation (#3129)\n* ENH: Restore resampling to surface GIFTIs (#3126)\n* ENH: Restore confound generation (#3120)\n* ENH: Restore resampling BOLD to volumetric templates (#3121)\n* ENH: Restore resampling to T1w target (#3116)\n* ENH: Add MSMSulc (#3085)\n* ENH: Add reporting workflow for BOLD fit (#3082)\n* ENH: Generate anatomical derivatives useful for resampling (#3081)\n* RF: Load reportlets interfaces from nireports rather than niworkflows (#3176, #3184)\n* RF: Separate goodvoxels mask creation from fsLR resampling (#3170)\n* RF: Write out anatomical template derivatives (#3136)\n* RF: Update primary bold workflow to incorporate single shot resampling (#3114)\n* RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078)\n* RF: Split fMRIPrep into fit and derivatives workflows (#2913)\n* RPT: Rename CSF/WM confounds in fMRIPlot (#3172)\n* TST: Add smoke tests for full workflow and most branching flags (#3155)\n* TST: Add smoke-tests for bold_fit_wf (#3152)\n* DOC: Fix documentation and description for init_bold_grayords_wf (#3051)\n* DOC: Minor updates in outputs.rst (#3148)\n* STY: Apply a couple refurb suggestions (#3151)\n* STY: Fix flake8 warnings (#3044)\n* STY: Apply pyupgrade suggestions (#3043)\n* MNT: Restore mritotal subcommands to Dockerfile (#3149)\n* MNT: Update smriprep to 0.13.1 (#3153)\n* MNT: optimise size of PNG files (#3145)\n* MNT: update vendored docs script ``github_link.py`` (#3144)\n* MNT: Update tedana pin, test on Python 3.12 (#3141)\n* MNT: Bump environment (#3132)\n* MNT: Bump version requirements (#3107)\n* MNT: http:// → https:// (#3097)\n* MNT: Remove mritotal and dependencies from FreeSurfer ignore file (#3090)\n* MNT: Update environment (#3073)\n* MNT: Depend on newer sphinx (#3067)\n* MNT: Install ANTs from conda-forge (#3061)\n* MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (#3052)\n* MNT: update update_zenodo.py script (#3042)\n* MNT: Fix welcome message formatting and instructions (#3039)\n* MNT: Python 3.11 should be supported (#3038)\n* CI: Bump actions/setup-python from 4 to 5 (#3181)\n* CI: Stop testing legacy layout (#3079)\n* CI: Improve tag detection for docker builds (#3066)\n* CI: Clean up pre-release builds (#3040)","shortMessageHtmlLink":"Merge tag '23.2.0' into deepprep"}},{"before":null,"after":"bfa25c35a90b42e5e71c40011073992ec2ddb023","ref":"refs/heads/deepprep","pushedAt":"2024-01-11T06:44:46.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"NingAnMe","name":"Ning An","path":"/NingAnMe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13708622?s=80&v=4"},"commit":{"message":"CHG: delete other processes","shortMessageHtmlLink":"CHG: delete other processes"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMi0wNVQxMzoyMjo0Mi4wMDAwMDBazwAAAAPySaut","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMS0xMVQwNjo0NDo0Ni4wMDAwMDBazwAAAAPc9_Xz"}},"title":"Activity · NingAnMe/fmriprep"}