{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/817","repository_url":"https://api.github.com/repos/poldracklab/fmriprep","labels_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/817/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/817/comments","events_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/817/events","html_url":"https://github.com/poldracklab/fmriprep/issues/817","id":272059907,"number":817,"title":"ICA AROMA: interacting with the other confounds","user":{"login":"jdkent","id":12564882,"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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":25,"created_at":"2017-11-08T03:07:29Z","updated_at":"2018-04-07T03:40:35Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"The standard way to use ICA-AROMA with non-aggressive denoising in conjunction with other confounds in the tsv (specifically acompcor, tcompcor, and other measures derived from the bold), is to pull out those signals **after** denoising of the data, as to not re-introduce noise removed by ICA-AROMA (if we calculated acompcor, tcompcor before ICA-denoising). So my question is: does this mean we should re-organize the code to also pass in the non-aggressively denoised bold to calculate these other measures? or would it be equivalent to do full regression removing the variance explained by the \"noise components\" on the other confounds in the tsv as I did in the final part of [this jupyter notebook](http://nbviewer.jupyter.org/github/jdkent/tests_and_musings/blob/master/Confound%20Regression.ipynb). The latter would be substantially easier, but I don't know if we are sacrificing something, or doing something not recommended. "},"comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/comments/379429260","html_url":"https://github.com/poldracklab/fmriprep/issues/817#issuecomment-379429260","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/817","id":379429260,"user":{"login":"chrisfilo","id":238759,"avatar_url":"https://avatars2.githubusercontent.com/u/238759?v=4","gravatar_id":"","url":"https://api.github.com/users/chrisfilo","html_url":"https://github.com/chrisfilo","followers_url":"https://api.github.com/users/chrisfilo/followers","following_url":"https://api.github.com/users/chrisfilo/following{/other_user}","gists_url":"https://api.github.com/users/chrisfilo/gists{/gist_id}","starred_url":"https://api.github.com/users/chrisfilo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrisfilo/subscriptions","organizations_url":"https://api.github.com/users/chrisfilo/orgs","repos_url":"https://api.github.com/users/chrisfilo/repos","events_url":"https://api.github.com/users/chrisfilo/events{/privacy}","received_events_url":"https://api.github.com/users/chrisfilo/received_events","type":"User","site_admin":false},"created_at":"2018-04-07T03:40:35Z","updated_at":"2018-04-07T03:40:35Z","author_association":"CONTRIBUTOR","body":"I'm not sure how you can do that with FMRIPREP. One thing is certain ICA AROMA depends on your data being in the MNI space (or being able to put it in the MNI space) because it uses ROIs defined in MNI.\r\n\r\nOut of curiosity which template are you using as coregistration target for your infant study?"}}
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