{"action":"created","comment":{"url":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/45972920","id":45972920,"diff_hunk":"@@ -0,0 +1,82 @@\n+\"\"\"\n+Regions extraction using Canonical ICA maps and functional connectomes\n+======================================================================\n+\n+This example shows how to use :class:`nilearn.regions.RegionExtractor`\n+to extract connected brain regions from whole brain ICA maps and\n+use them to estimate a connectome.\n+\n+We used 20 resting state ADHD functional datasets from :func:`nilearn.datasets.fetch_adhd`\n+and :class:`nilearn.decomposition.CanICA` for whole brain ICA maps.\n+\n+Please see the related documentation of :class:`nilearn.regions.RegionExtractor`\n+for more details.\n+\"\"\"\n+import numpy as np\n+from nilearn import datasets\n+print(\" -- Fetching ADHD resting state functional datasets -- \")\n+adhd_dataset = datasets.fetch_adhd(n_subjects=20)\n+func_filenames = adhd_dataset.func\n+confounds = adhd_dataset.confounds\n+\n+from nilearn.decomposition import CanICA\n+print(\" -- Canonical ICA decomposition of functional datasets -- \")\n+# Initialize canica parameters\n+n_components = 8\n+canica = CanICA(n_components=n_components, smoothing_fwhm=6.,\n+                memory=\"nilearn_cache\", memory_level=2,\n+                random_state=0)\n+\n+canica.fit(func_filenames)\n+components_img = canica.masker_.inverse_transform(canica.components_)\n+\n+from nilearn.regions import region_extractor\n+print(\" -- Extracting regions from ICA maps and timeseries signals -- \")\n+extractor = region_extractor.RegionExtractor(\n+    components_img, threshold=0.5, thresholding_strategy='ratio_n_voxels',\n+    standardize=True, min_region_size=100)\n+# Regions extraction from ICA maps\n+extractor.fit()\n+regions_extracted = extractor.regions_\n+n_regions = regions_extracted.shape[3]\n+print(\" ====== Regions extracted ====== \")\n+print(\" -- %d regions are extracted from %d ICA components -- \" % (\n+    n_components, n_regions))","path":"examples/connectivity/plot_extract_regions_canica_maps.py","position":44,"original_position":44,"commit_id":"2d4daa7bff59d0d1995fe8480134ae45410847e4","original_commit_id":"2d4daa7bff59d0d1995fe8480134ae45410847e4","user":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"body":"Oops, this need to be changed.","created_at":"2015-11-26T12:21:14Z","updated_at":"2015-11-26T12:21:14Z","html_url":"https://github.com/nilearn/nilearn/pull/651#discussion_r45972920","pull_request_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651","_links":{"self":{"href":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/45972920"},"html":{"href":"https://github.com/nilearn/nilearn/pull/651#discussion_r45972920"},"pull_request":{"href":"https://api.github.com/repos/nilearn/nilearn/pulls/651"}}},"pull_request":{"url":"https://api.github.com/repos/nilearn/nilearn/pulls/651","id":39828251,"html_url":"https://github.com/nilearn/nilearn/pull/651","diff_url":"https://github.com/nilearn/nilearn/pull/651.diff","patch_url":"https://github.com/nilearn/nilearn/pull/651.patch","issue_url":"https://api.github.com/repos/nilearn/nilearn/issues/651","number":651,"state":"open","locked":false,"title":"[MRG] Region 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Code\r\n- [x] Documentation\r\n- [x] Tests\r\n- [x] Example\r\n\r\n* Code design\r\n   * ```class``` named as ```RegionExtractor``` - to *extract regions* from the maps and also extracts *subjects timeseries signals* from those extracted regions by inheriting ```NiftiMapsMasker```.\r\n         * function named as ```threshold_img``` to keep meaningful voxels for region extraction.\r\n         * function named as ```connected_regions``` to extract regions from thresholded images.\r\n\r\n*  ``` RegionExtractor ```\r\n      * ```fit()``` extract regions.\r\n      * ```transform()``` regions to signals.\r\n         * example: ```plot_extract_regions_canica_maps.py``` \r\n         * example: ```plot_extract_regions_smith_atlas_networks.py```\r\n\r\n*  ```threshold_img``` - two different ways of thresholding. (integrated in ```nilearn.image.image```)\r\n      1. ```percentile``` - ```scoreatpercentile```.\r\n      2. ```img_value``` - based on voxel intensity value.\r\n          * example: ```plot_extract_regions_statistical_maps.py```\r\n\r\n*  ```connected_regions``` - two different ways of extracting regions.\r\n      1. ```local_regions``` uses random walker method.\r\n      2. ```connected_components``` uses only labelling which labels based on unique features. \r\n           * example: ```plot_extract_regions_statistical_maps.py```\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n","created_at":"2015-07-13T16:08:17Z","updated_at":"2015-11-26T12:21:14Z","closed_at":null,"merged_at":null,"merge_commit_sha":"386ff8bfa2b2f868f838aac012cf36812bfceef5","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651/commits","review_comments_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651/comments","review_comment_url":"https://api.github.com/repos/nilearn/nilearn/pulls/comments{/number}","comments_url":"https://api.github.com/repos/nilearn/nilearn/issues/651/comments","statuses_url":"https://api.github.com/repos/nilearn/nilearn/statuses/2d4daa7bff59d0d1995fe8480134ae45410847e4","head":{"label":"KamalakerDadi:AutoExtractor","ref":"AutoExtractor","sha":"2d4daa7bff59d0d1995fe8480134ae45410847e4","user":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"repo":{"id":32379132,"name":"nilearn","full_name":"KamalakerDadi/nilearn","owner":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/KamalakerDadi/nilearn","description":"Machine 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