{"action":"created","comment":{"url":"https://api.github.com/repos/brainiak/brainiak/pulls/comments/209363969","pull_request_review_id":145372062,"id":209363969,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwOTM2Mzk2OQ==","diff_hunk":"@@ -1382,7 +1478,7 @@ def generate_noise_volume(dimensions,\n                                                              1)\n     temporal_noise = temporal_noise - (temporal_noise_mean - spatial_noise)","path":"brainiak/utils/fmrisim.py","position":null,"original_position":576,"commit_id":"f9c7ff1f849400baeddcb4e9a3ddeb9ca592a718","original_commit_id":"2cf25818ec99e54760552d7fec38ef58c6177913","user":{"login":"lcnature","id":7763789,"node_id":"MDQ6VXNlcjc3NjM3ODk=","avatar_url":"https://avatars2.githubusercontent.com/u/7763789?v=4","gravatar_id":"","url":"https://api.github.com/users/lcnature","html_url":"https://github.com/lcnature","followers_url":"https://api.github.com/users/lcnature/followers","following_url":"https://api.github.com/users/lcnature/following{/other_user}","gists_url":"https://api.github.com/users/lcnature/gists{/gist_id}","starred_url":"https://api.github.com/users/lcnature/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lcnature/subscriptions","organizations_url":"https://api.github.com/users/lcnature/orgs","repos_url":"https://api.github.com/users/lcnature/repos","events_url":"https://api.github.com/users/lcnature/events{/privacy}","received_events_url":"https://api.github.com/users/lcnature/received_events","type":"User","site_admin":false},"body":"I see you point. So `spatial_sd` only matters when there are multiple runs. If there is a single run, it is undetectable since no one knows the real intensity at each voxel. Then I agree that temporal_noise is sufficient. It would only be a bit odd if the baseline outside of the brain are all set zero and temporal_noise is also demeaned - which makes every voxel's temporal mean strictly zero - which is unlikely but probably no one cares much. If you do not demean temporal_noise, then it seems fine.\r\nAbout `_calc_snr`, I think it is called by `_fit_spatial` in 2362 with the input `noise`, and the `noise` fed to `_fit_spatial` in line 2761 seems to be a spatial-temporal matrix. So I think `_calc_snr` actually deals with 4D data. And I *think* the resulting SNR is based on the spatial variation of temporally demeaned noise.\r\n\r\n","created_at":"2018-08-10T19:32:33Z","updated_at":"2018-08-10T19:32:33Z","html_url":"https://github.com/brainiak/brainiak/pull/372#discussion_r209363969","pull_request_url":"https://api.github.com/repos/brainiak/brainiak/pulls/372","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/brainiak/brainiak/pulls/comments/209363969"},"html":{"href":"https://github.com/brainiak/brainiak/pull/372#discussion_r209363969"},"pull_request":{"href":"https://api.github.com/repos/brainiak/brainiak/pulls/372"}},"in_reply_to_id":208628502},"pull_request":{"url":"https://api.github.com/repos/brainiak/brainiak/pulls/372","id":192576468,"node_id":"MDExOlB1bGxSZXF1ZXN0MTkyNTc2NDY4","html_url":"https://github.com/brainiak/brainiak/pull/372","diff_url":"https://github.com/brainiak/brainiak/pull/372.diff","patch_url":"https://github.com/brainiak/brainiak/pull/372.patch","issue_url":"https://api.github.com/repos/brainiak/brainiak/issues/372","number":372,"state":"open","locked":false,"title":"Fit parameters","user":{"login":"CameronTEllis","id":11008543,"node_id":"MDQ6VXNlcjExMDA4NTQz","avatar_url":"https://avatars3.githubusercontent.com/u/11008543?v=4","gravatar_id":"","url":"https://api.github.com/users/CameronTEllis","html_url":"https://github.com/CameronTEllis","followers_url":"https://api.github.com/users/CameronTEllis/followers","following_url":"https://api.github.com/users/CameronTEllis/following{/other_user}","gists_url":"https://api.github.com/users/CameronTEllis/gists{/gist_id}","starred_url":"https://api.github.com/users/CameronTEllis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/CameronTEllis/subscriptions","organizations_url":"https://api.github.com/users/CameronTEllis/orgs","repos_url":"https://api.github.com/users/CameronTEllis/repos","events_url":"https://api.github.com/users/CameronTEllis/events{/privacy}","received_events_url":"https://api.github.com/users/CameronTEllis/received_events","type":"User","site_admin":false},"body":"Added the ability to fit SFNR, SNR and AR noise parameters. 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