{"action":"created","comment":{"url":"https://api.github.com/repos/poldracklab/niworkflows/pulls/comments/191654728","pull_request_review_id":124264231,"id":191654728,"diff_hunk":"@@ -237,7 +237,7 @@ def _get_dataset_dir(dataset_name, data_dir=None, default_paths=None,\n     # Search possible system paths\n     if default_paths is not None:\n         for default_path in default_paths:\n-            paths.extend([(d, True) for d in default_path.split(os.pathsep)])\n+            paths.extend([(d, True) for d in default_paths.split(os.pathsep)])","path":"niworkflows/data/utils.py","position":5,"original_position":5,"commit_id":"1e2cffb7d55412c7e32b2750ae0874ab88931d67","original_commit_id":"1e2cffb7d55412c7e32b2750ae0874ab88931d67","user":{"login":"oesteban","id":598470,"avatar_url":"https://avatars2.githubusercontent.com/u/598470?v=4","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},"body":"Yep","created_at":"2018-05-30T06:31:51Z","updated_at":"2018-05-30T06:31:51Z","html_url":"https://github.com/poldracklab/niworkflows/pull/244#discussion_r191654728","pull_request_url":"https://api.github.com/repos/poldracklab/niworkflows/pulls/244","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/poldracklab/niworkflows/pulls/comments/191654728"},"html":{"href":"https://github.com/poldracklab/niworkflows/pull/244#discussion_r191654728"},"pull_request":{"href":"https://api.github.com/repos/poldracklab/niworkflows/pulls/244"}},"in_reply_to_id":191615987},"pull_request":{"url":"https://api.github.com/repos/poldracklab/niworkflows/pulls/244","id":191042873,"html_url":"https://github.com/poldracklab/niworkflows/pull/244","diff_url":"https://github.com/poldracklab/niworkflows/pull/244.diff","patch_url":"https://github.com/poldracklab/niworkflows/pull/244.patch","issue_url":"https://api.github.com/repos/poldracklab/niworkflows/issues/244","number":244,"state":"open","locked":false,"title":"[ENH] Nipype-fy ``antsBrainExtraction.sh``","user":{"login":"oesteban","id":598470,"avatar_url":"https://avatars2.githubusercontent.com/u/598470?v=4","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},"body":"This will enable several steps towards generalization:\r\n\r\n  - Play with the template used as target for brain extraction (e.g. macaque, mice)\r\n  - Have more control over settings (important for templates of other species)\r\n  - Use the transforms to the target template (e.g. to initialize the spatial normalization)\r\n  - Revise the brain mask refinements\r\n  - Closely control over what ANTs is doing to headers.\r\n  - (probably we will not notice) leverage nipype parallelization and caching\r\n  - Refine ATROPOS results and merge results with FAST (smoother segmentations)\r\n\r\nEDIT: **PLEASE NOTE** that this PR will change how the templates are accessed, trying to normalize naming. So far only two templates are supported, and their tree is like:\r\n\r\n```Tree\r\ntpl-MNI152NLin2009cAsym\r\n├── CHANGES\r\n├── template_description.json\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_brainmask.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-CSF_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-GM_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-WM_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-carpet_atlas.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-eyemask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-facemask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-headmask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_PD.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w_brain.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T2w.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-CSF_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-GM_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-WM_probtissue.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-carpet_atlas.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-eyemask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-facemask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-headmask_roi.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_PD.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T1w_brain.nii.gz\r\n├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T1w.nii.gz\r\n└── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T2w.nii.gz\r\ntpl-OASIS30ANTs\r\n├── CHANGES\r\n├── template_description.json\r\n├── tpl-OASIS30ANTs_res-01_brainmask.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-brainmask_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-bstem_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-Cerebellum_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-CGM_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-CSF_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-DGM_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_class-WM_probtissue.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_label-BrainCerebellumExtraction_roi.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_label-BrainCerebellumRegistration_roi.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_T1w_brain.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_T1w.nii.gz\r\n├── tpl-OASIS30ANTs_res-01_variant-4_dtissue.nii.gz\r\n└── tpl-OASIS30ANTs_res-01_variant-6_dtissue.nii.gz\r\n```\r\n\r\nI've also taken time to clean all these files up, fixing appropriate dtypes, filling wrong headers, copying the sforms to the qforms, 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