{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/356","repository_url":"https://api.github.com/repos/poldracklab/fmriprep","labels_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/356/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/356/comments","events_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/356/events","html_url":"https://github.com/poldracklab/fmriprep/issues/356","id":206680704,"number":356,"title":"Restructuring outputs","user":{"login":"chrisfilo","id":238759,"avatar_url":"https://avatars.githubusercontent.com/u/238759?v=3","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-02-10T01:22:46Z","updated_at":"2017-02-13T22:32:32Z","closed_at":null,"body":"Right now if someone runs `fmriprep /bids_directory /outputs participant` they get the following:\r\n\r\n```\r\n|-- derivatives\r\n|   `-- sub-387\r\n|       |-- anat\r\n|       |   |-- sub-387_T1w_brainmask.nii.gz\r\n|       |   |-- sub-387_T1w_dtissue.nii.gz\r\n|       |   |-- sub-387_T1w_preproc.nii.gz\r\n|       |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz\r\n|       |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz\r\n|       |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz\r\n|       |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz\r\n|       |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz\r\n|       |   |-- sub-387_T1w_target-MNI152NLin2009cAsym_affine.mat\r\n|       |   |-- sub-387_T1w_target-MNI152NLin2009cAsym_warp.nii.gz\r\n|       |   `-- sub-387_T1w_target-meanBOLD_affine.txt\r\n|       `-- func\r\n|           |-- sub-387_task-Beast_run-1_bold_brainmask.nii.gz\r\n|           |-- sub-387_task-Beast_run-1_bold_confounds.tsv\r\n|           |-- sub-387_task-Beast_run-1_bold_preproc.nii.gz\r\n|           |-- sub-387_task-Beast_run-1_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz\r\n|           |-- sub-387_task-Beast_run-1_bold_space-MNI152NLin2009cAsym_preproc.nii.gz\r\n|           `-- sub-387_task-Beast_run-1_bold_target-T1w_affine.txt\r\n|-- log\r\n|   `-- run_workflow\r\n|-- reports\r\n|   `-- sub-387\r\n|       |-- anat\r\n|       |   |-- sub-387_T1w_t1_2_mni.svg\r\n|       |   |-- sub-387_T1w_t1_seg.html\r\n|       |   `-- sub-387_T1w_t1_skull_strip.html\r\n|       `-- func\r\n|           |-- sub-387_task-Beast_run-1_bold_acompcor.html\r\n|           |-- sub-387_task-Beast_run-1_bold_bet_hmc.html\r\n|           |-- sub-387_task-Beast_run-1_bold_flt_bbr.svg\r\n|           `-- sub-387_task-Beast_run-1_bold_tcompcor.html\r\n`-- sub-387.html\r\n```\r\n\r\nI would propose refactoring this to the following (with inclusion of recon-all outputs #347 ):\r\n\r\n```\r\n|-- freesurfer\r\n|   |-- README\r\n|   |-- pipeline_description.json\r\n|   `-- sub-338\r\n|       |-- label\r\n|       |-- mri\r\n|       |-- scripts\r\n|       |-- stats\r\n|       |-- surf\r\n|       |-- tmp\r\n|       |-- touch\r\n|       `-- trash\r\n`-- fmriprep\r\n    |-- README\r\n    |-- pipeline_description.json\r\n    |-- sub-387\r\n    |   |-- anat\r\n    |   |   |-- sub-387_T1w_brainmask.nii.gz\r\n    |   |   |-- sub-387_T1w_dtissue.nii.gz\r\n    |   |   |-- sub-387_T1w_preproc.nii.gz\r\n    |   |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz\r\n    |   |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz\r\n    |   |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz\r\n    |   |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz\r\n    |   |   |-- sub-387_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz\r\n    |   |   |-- sub-387_T1w_target-MNI152NLin2009cAsym_affine.mat\r\n    |   |   |-- sub-387_T1w_target-MNI152NLin2009cAsym_warp.nii.gz\r\n    |   |   `-- sub-387_T1w_target-meanBOLD_affine.txt\r\n    |   `-- func\r\n    |       |-- sub-387_task-Beast_run-1_bold_brainmask.nii.gz\r\n    |       |-- sub-387_task-Beast_run-1_bold_confounds.tsv\r\n    |       |-- sub-387_task-Beast_run-1_bold_preproc.nii.gz\r\n    |       |-- sub-387_task-Beast_run-1_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz\r\n    |       |-- sub-387_task-Beast_run-1_bold_space-MNI152NLin2009cAsym_preproc.nii.gz\r\n    |       `-- sub-387_task-Beast_run-1_bold_target-T1w_affine.txt\r\n    `-- sub-387.html\r\n```\r\n\r\nMost notable differences:\r\n\r\n- Removal of subworkflows (end user does not need them - let's keep them in the ephemeral working directory)\r\n- Removal of `log` subdirectory (the log is actually empty)\r\n- Keeping recon-all and mriqc separate\r\n- Ability to run `fmriprep /bids_directory /bids_directory/derivatives participant` and getting a dataset compatible with [BIDS Derivatives](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit#heading=h.4xwnp2872y57)\r\n\r\nLet me know what do you think."},"comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/comments/279545171","html_url":"https://github.com/poldracklab/fmriprep/issues/356#issuecomment-279545171","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/356","id":279545171,"user":{"login":"oesteban","id":598470,"avatar_url":"https://avatars.githubusercontent.com/u/598470?v=3","gravatar_id":"","url":"https://api.github.com/users/oesteban","html_url":"https://github.com/oesteban","followers_url":"https://api.github.com/users/oesteban/followers","following_url":"https://api.github.com/users/oesteban/following{/other_user}","gists_url":"https://api.github.com/users/oesteban/gists{/gist_id}","starred_url":"https://api.github.com/users/oesteban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oesteban/subscriptions","organizations_url":"https://api.github.com/users/oesteban/orgs","repos_url":"https://api.github.com/users/oesteban/repos","events_url":"https://api.github.com/users/oesteban/events{/privacy}","received_events_url":"https://api.github.com/users/oesteban/received_events","type":"User","site_admin":false},"created_at":"2017-02-13T22:32:32Z","updated_at":"2017-02-13T22:32:32Z","body":"Worth looking at [this very simple test](https://github.com/oesteban/mriqc/blob/master/circle.yml#L34) I've added to mriqc to check that all the desired outputs are there, with the correct naming."}}
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