{"action":"created","comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments/227204458","pull_request_review_id":167179492,"id":227204458,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIyNzIwNDQ1OA==","diff_hunk":"@@ -586,18 +612,67 @@ def _getbtthresh(medianval):\n         (melodic, ica_aroma, [('out_dir', 'melodic_dir')]),\n         # generate tsvs from ICA-AROMA\n         (ica_aroma, ica_aroma_confound_extraction, [('out_dir', 'in_directory')]),\n+        (inputnode, ica_aroma_confound_extraction, [\n+            ('skip_vols', 'skip_vols')]),\n         # output for processing and reporting\n         (ica_aroma_confound_extraction, outputnode, [('aroma_confounds', 'aroma_confounds'),\n                                                      ('aroma_noise_ics', 'aroma_noise_ics'),\n                                                      ('melodic_mix', 'melodic_mix')]),\n         # TODO change melodic report to reflect noise and non-noise components\n-        (ica_aroma, outputnode, [('nonaggr_denoised_file', 'nonaggr_denoised_file')]),\n+        (ica_aroma, add_non_steady_state, [\n+            ('nonaggr_denoised_file', 'bold_cut_file')]),\n+        (bold_mni_trans_wf, add_non_steady_state, [\n+            ('outputnode.bold_mni', 'bold_file')]),\n+        (inputnode, add_non_steady_state, [\n+            ('skip_vols', 'skip_vols')]),\n+        (add_non_steady_state, outputnode, [('bold_add', 'nonaggr_denoised_file')]),\n         (ica_aroma, ds_report_ica_aroma, [('out_report', 'in_file')]),\n     ])\n \n     return workflow\n \n \n+def _remove_volumes(bold_file, skip_vols):\n+        import nibabel as nb\n+        from nipype.utils.filemanip import fname_presuffix\n+\n+        # load the bold file and get the 4d matrix","path":"fmriprep/workflows/bold/confounds.py","position":234,"original_position":234,"commit_id":"11ea1c24c39812f0c05fc4a6e4827da6d381ac10","original_commit_id":"11ea1c24c39812f0c05fc4a6e4827da6d381ac10","user":{"login":"effigies","id":83442,"node_id":"MDQ6VXNlcjgzNDQy","avatar_url":"https://avatars0.githubusercontent.com/u/83442?v=4","gravatar_id":"","url":"https://api.github.com/users/effigies","html_url":"https://github.com/effigies","followers_url":"https://api.github.com/users/effigies/followers","following_url":"https://api.github.com/users/effigies/following{/other_user}","gists_url":"https://api.github.com/users/effigies/gists{/gist_id}","starred_url":"https://api.github.com/users/effigies/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/effigies/subscriptions","organizations_url":"https://api.github.com/users/effigies/orgs","repos_url":"https://api.github.com/users/effigies/repos","events_url":"https://api.github.com/users/effigies/events{/privacy}","received_events_url":"https://api.github.com/users/effigies/received_events","type":"User","site_admin":false},"body":"Before doing anything else, I would check:\r\n\r\n```Python\r\nif skip_vols == 0:\r\n    return bold_file\r\n```","created_at":"2018-10-23T02:42:26Z","updated_at":"2018-10-23T02:46:59Z","html_url":"https://github.com/poldracklab/fmriprep/pull/1335#discussion_r227204458","pull_request_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1335","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments/227204458"},"html":{"href":"https://github.com/poldracklab/fmriprep/pull/1335#discussion_r227204458"},"pull_request":{"href":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1335"}}},"pull_request":{"url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1335","id":224444864,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI0NDQ0ODY0","html_url":"https://github.com/poldracklab/fmriprep/pull/1335","diff_url":"https://github.com/poldracklab/fmriprep/pull/1335.diff","patch_url":"https://github.com/poldracklab/fmriprep/pull/1335.patch","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1335","number":1335,"state":"open","locked":false,"title":"[FIX]: remove non steady-state volumes from aroma calculation","user":{"login":"jdkent","id":12564882,"node_id":"MDQ6VXNlcjEyNTY0ODgy","avatar_url":"https://avatars0.githubusercontent.com/u/12564882?v=4","gravatar_id":"","url":"https://api.github.com/users/jdkent","html_url":"https://github.com/jdkent","followers_url":"https://api.github.com/users/jdkent/followers","following_url":"https://api.github.com/users/jdkent/following{/other_user}","gists_url":"https://api.github.com/users/jdkent/gists{/gist_id}","starred_url":"https://api.github.com/users/jdkent/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdkent/subscriptions","organizations_url":"https://api.github.com/users/jdkent/orgs","repos_url":"https://api.github.com/users/jdkent/repos","events_url":"https://api.github.com/users/jdkent/events{/privacy}","received_events_url":"https://api.github.com/users/jdkent/received_events","type":"User","site_admin":false},"body":"<!--\r\nText in these brackets are comments, and won't be visible when you submit your pull request.\r\nIf this is your first contribution, please take the time to read these, in particular the comment\r\nbeginning \"Welcome, new contributors!\".\r\n-->\r\n\r\n## Changes proposed in this pull request\r\nref #1136\r\nref #1300\r\n<!--\r\nPlease describe here the main features / changes proposed for review and integration in fMRIPrep\r\nIf this PR addresses some existing problem, please use GitHub's citing tools \r\n(eg. ref #, closes # or fixes #).\r\nIf there is not an existing issue open describing the problem, please consider opening a new\r\nissue first and then link it from here (so the *fMRIPrep* community has a better understanding\r\nof ongoing development efforts and possible overlaps between contributions).\r\n-->\r\nThis pull request pulls the steady state detector into `bold/base.py` and uses it's output for both the confounds workflow and the aroma workflow.\r\n\r\n## Documentation that should be reviewed\r\n<!--\r\nPlease summarize here the main changes to the documentation that the reviewers should be aware of.\r\n-->\r\nI need to update the documentation for ica-aroma, more details to come...\r\n\r\n\r\n<!--\r\nWelcome, new contributors!\r\n\r\nWe ask you to read through the Contributing Guide:\r\nhttps://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md\r\n\r\nThese are guidelines intended to make communication easier by describing a consistent process, but\r\ndon't worry if you don't get it everything exactly \"right\" on the first try.\r\n\r\nTo boil it down, here are some highlights:\r\n\r\n1) Consider starting a conversation in the issues list before submitting a pull request. The discussion might save you a\r\n   lot of time coding.\r\n2) Please use descriptive prefixes in your pull request title, such as \"ENH:\" for an enhancement or \"FIX:\" for a bug fix.\r\n   (See the Contributing guide for the full set.) And consider adding a \"WIP\" tag for works-in-progress.\r\n3) Any code you submit will be licensed under the same terms (BSD 3-Clause) as the rest of fMRIPrep.\r\n4) We invite every contributor to add themselves to the `.zenodo.json` file\r\n   (https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json), which will result in your being listed as an author\r\n   at the next release. Please add yourself as the next-to-last entry, just above Russ.\r\n\r\nA pull request is a conversation. We may ask you to make some changes before accepting your PR,\r\nand likewise, you should feel free to ask us any questions you have.\r\n\r\n-->\r\n","created_at":"2018-10-20T01:59:22Z","updated_at":"2018-10-23T02:46:59Z","closed_at":null,"merged_at":null,"merge_commit_sha":"8ad5aed4679249d4eb932f273903ac2b308eed06","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1335/commits","review_comments_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1335/comments","review_comment_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments{/number}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1335/comments","statuses_url":"https://api.github.com/repos/poldracklab/fmriprep/statuses/11ea1c24c39812f0c05fc4a6e4827da6d381ac10","head":{"label":"jdkent:remove_init_vol_aroma","ref":"remove_init_vol_aroma","sha":"11ea1c24c39812f0c05fc4a6e4827da6d381ac10","user":{"login":"jdkent","id":12564882,"node_id":"MDQ6VXNlcjEyNTY0ODgy","avatar_url":"https://avatars0.githubusercontent.com/u/12564882?v=4","gravatar_id":"","url":"https://api.github.com/users/jdkent","html_url":"https://github.com/jdkent","followers_url":"https://api.github.com/users/jdkent/followers","following_url":"https://api.github.com/users/jdkent/following{/other_user}","gists_url":"https://api.github.com/users/jdkent/gists{/gist_id}","starred_url":"https://api.github.com/users/jdkent/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdkent/subscriptions","organizations_url":"https://api.github.com/users/jdkent/orgs","repos_url":"https://api.github.com/users/jdkent/repos","events_url":"https://api.github.com/users/jdkent/events{/privacy}","received_events_url":"https://api.github.com/users/jdkent/received_events","type":"User","site_admin":false},"repo":{"id":92465059,"node_id":"MDEwOlJlcG9zaXRvcnk5MjQ2NTA1OQ==","name":"fmriprep","full_name":"jdkent/fmriprep","private":false,"owner":{"login":"jdkent","id":12564882,"node_id":"MDQ6VXNlcjEyNTY0ODgy","avatar_url":"https://avatars0.githubusercontent.com/u/12564882?v=4","gravatar_id":"","url":"https://api.github.com/users/jdkent","html_url":"https://github.com/jdkent","followers_url":"https://api.github.com/users/jdkent/followers","following_url":"https://api.github.com/users/jdkent/following{/other_user}","gists_url":"https://api.github.com/users/jdkent/gists{/gist_id}","starred_url":"https://api.github.com/users/jdkent/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdkent/subscriptions","organizations_url":"https://api.github.com/users/jdkent/orgs","repos_url":"https://api.github.com/users/jdkent/repos","events_url":"https://api.github.com/users/jdkent/events{/privacy}","received_events_url":"https://api.github.com/users/jdkent/received_events","type":"User","site_admin":false},"html_url":"https://github.com/jdkent/fmriprep","description":"fMRIprep 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