{"action":"created","issue":{"url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/785","repository_url":"https://api.github.com/repos/MRtrix3/mrtrix3","labels_url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/785/labels{/name}","comments_url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/785/comments","events_url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/785/events","html_url":"https://github.com/MRtrix3/mrtrix3/pull/785","id":178780034,"number":785,"title":"Tag 0.3.16","user":{"login":"Lestropie","id":5637955,"avatar_url":"https://avatars.githubusercontent.com/u/5637955?v=3","gravatar_id":"","url":"https://api.github.com/users/Lestropie","html_url":"https://github.com/Lestropie","followers_url":"https://api.github.com/users/Lestropie/followers","following_url":"https://api.github.com/users/Lestropie/following{/other_user}","gists_url":"https://api.github.com/users/Lestropie/gists{/gist_id}","starred_url":"https://api.github.com/users/Lestropie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Lestropie/subscriptions","organizations_url":"https://api.github.com/users/Lestropie/orgs","repos_url":"https://api.github.com/users/Lestropie/repos","events_url":"https://api.github.com/users/Lestropie/events{/privacy}","received_events_url":"https://api.github.com/users/Lestropie/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/MRtrix3/mrtrix3/milestones/1","html_url":"https://github.com/MRtrix3/mrtrix3/milestone/1","labels_url":"https://api.github.com/repos/MRtrix3/mrtrix3/milestones/1/labels","id":1036648,"number":1,"title":"MRtrix3 3.0 release ","description":"","creator":{"login":"jdtournier","id":3221000,"avatar_url":"https://avatars.githubusercontent.com/u/3221000?v=3","gravatar_id":"","url":"https://api.github.com/users/jdtournier","html_url":"https://github.com/jdtournier","followers_url":"https://api.github.com/users/jdtournier/followers","following_url":"https://api.github.com/users/jdtournier/following{/other_user}","gists_url":"https://api.github.com/users/jdtournier/gists{/gist_id}","starred_url":"https://api.github.com/users/jdtournier/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdtournier/subscriptions","organizations_url":"https://api.github.com/users/jdtournier/orgs","repos_url":"https://api.github.com/users/jdtournier/repos","events_url":"https://api.github.com/users/jdtournier/events{/privacy}","received_events_url":"https://api.github.com/users/jdtournier/received_events","type":"User","site_admin":false},"open_issues":19,"closed_issues":149,"state":"open","created_at":"2015-03-24T16:09:24Z","updated_at":"2017-02-22T12:24:14Z","due_on":"2016-08-31T07:00:00Z","closed_at":null},"comments":65,"created_at":"2016-09-23T04:07:01Z","updated_at":"2017-02-23T03:50:22Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/MRtrix3/mrtrix3/pulls/785","html_url":"https://github.com/MRtrix3/mrtrix3/pull/785","diff_url":"https://github.com/MRtrix3/mrtrix3/pull/785.diff","patch_url":"https://github.com/MRtrix3/mrtrix3/pull/785.patch"},"body":"OK, have started the branch that will be eventually merged to master to form tag 0.3.16, which _should_ be the last tag before release (I think I've said that before though...). It will be a bit of an agglomeration of all sorts of things, but the primary one is getting the new fixel format pushed out and tested.\n\nMain changes already in this branch:\n- Changes to mesh handling code: Not really anything new, just making it all more modular for future enhancements. Can now import FreeSurfer meshes (in code at least).\n- Everything that was in the `stanford` branch. This includes:\n  - Fixing all statistics code to use double precision (except for CFE connectivities), and getting some code into `.cpp` files to reduce RAM usage / increase parallelism in compilation. Also changes certain structures and whatnot to improve compatibility with non-CFE stats code usage. Supersedes #701.\n  - `mrhistmatch`: Non-linear histogram matching (#671).\n  - `connectomestats`: NBSE method (#723).\n  - `vectorstats`: Basically does permutation testing on 1D data (#724).\n  - NIfTI-2 support (#19).\n  - JSON file support, as provided by JSON for Modern C++ (#725).\n  - Get phase encoding information from DICOM and store in header (#725).\n  - `dwipreproc`: Complete internal re-design, including using phase encoding information from image headers to set up `topup`/`eddy` (#747).\n\nThings that still need to be merged in / could potentially be merged in / need development / testing:\n- New fixel format (#620). Close from what I hear.\n- System signal handlers (#776, #758): Awaiting confirmation that @jdtournier is content with the implementation. Would be nice to set up similar handlers for the Python scripts, but that can wait.\n- `dwipreproc` needs testing - I've done what I can, it would be nice if others try to break it. Also need to pick a better name for `-topup_images` option; I'm thinking something like `se_epi_field_images` since dual gradient echo-based field images could theoretically be used, but wouldn't work with this particular option.\n  Edit: Have changed it to simply `-se_epi`; complain if you don't like it.\n- Need to test DICOM phase encoding info import: Acquire SE EPIs with axial / sagittal / coronal slices, all 4 possible phase encoding directions for each.\n- Need those with non-Siemens data to figure out how other vendors provide the phase-encoding information in DICOMs and set up the import appropriately.\n- 'Stashing' `dw_scheme` once it no longer applies to the image volumes (#774): Let's pick a name.\n- `dwigradcheck` (#534): Since the problem has come up on the forum a few times, this would be useful to have. It's still a bit preliminary though. @bjeurissen Keen to put some effort into this?\n"},"comment":{"url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/comments/281886941","html_url":"https://github.com/MRtrix3/mrtrix3/pull/785#issuecomment-281886941","issue_url":"https://api.github.com/repos/MRtrix3/mrtrix3/issues/785","id":281886941,"user":{"login":"thijsdhollander","id":11952694,"avatar_url":"https://avatars.githubusercontent.com/u/11952694?v=3","gravatar_id":"","url":"https://api.github.com/users/thijsdhollander","html_url":"https://github.com/thijsdhollander","followers_url":"https://api.github.com/users/thijsdhollander/followers","following_url":"https://api.github.com/users/thijsdhollander/following{/other_user}","gists_url":"https://api.github.com/users/thijsdhollander/gists{/gist_id}","starred_url":"https://api.github.com/users/thijsdhollander/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thijsdhollander/subscriptions","organizations_url":"https://api.github.com/users/thijsdhollander/orgs","repos_url":"https://api.github.com/users/thijsdhollander/repos","events_url":"https://api.github.com/users/thijsdhollander/events{/privacy}","received_events_url":"https://api.github.com/users/thijsdhollander/received_events","type":"User","site_admin":false},"created_at":"2017-02-23T03:50:22Z","updated_at":"2017-02-23T03:50:22Z","body":"So 2 completely separate things to mention.  I'll start with just one of them (@Lestropie is probably looking into it right now).\r\n\r\n> There is one remaining gotcha that I didn't clean up. Any script that calls another Python script using run.command() (dwi2response dhollander and dwi2response msmt_5tt, I suppose dwiintensitynorm as well) will fail on Python 2.7 on Windows: subprocess rejects the target as a non-Win32 application. :-/ This I don't think is a 'new' problem though, just something that hadn't been found yet.\r\n\r\n...this just happened on our servers as well (i.e. not Windows)."}}
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