{"action":"created","issue":{"url":"https://api.github.com/repos/ANTsX/ANTs/issues/625","repository_url":"https://api.github.com/repos/ANTsX/ANTs","labels_url":"https://api.github.com/repos/ANTsX/ANTs/issues/625/labels{/name}","comments_url":"https://api.github.com/repos/ANTsX/ANTs/issues/625/comments","events_url":"https://api.github.com/repos/ANTsX/ANTs/issues/625/events","html_url":"https://github.com/ANTsX/ANTs/issues/625","id":351355112,"node_id":"MDU6SXNzdWUzNTEzNTUxMTI=","number":625,"title":"Brain Extraction - Intracranial Space","user":{"login":"jsebgiudice","id":42451197,"node_id":"MDQ6VXNlcjQyNDUxMTk3","avatar_url":"https://avatars1.githubusercontent.com/u/42451197?v=4","gravatar_id":"","url":"https://api.github.com/users/jsebgiudice","html_url":"https://github.com/jsebgiudice","followers_url":"https://api.github.com/users/jsebgiudice/followers","following_url":"https://api.github.com/users/jsebgiudice/following{/other_user}","gists_url":"https://api.github.com/users/jsebgiudice/gists{/gist_id}","starred_url":"https://api.github.com/users/jsebgiudice/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsebgiudice/subscriptions","organizations_url":"https://api.github.com/users/jsebgiudice/orgs","repos_url":"https://api.github.com/users/jsebgiudice/repos","events_url":"https://api.github.com/users/jsebgiudice/events{/privacy}","received_events_url":"https://api.github.com/users/jsebgiudice/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-08-16T20:24:00Z","updated_at":"2018-11-06T18:36:06Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI'm trying to construct a 3D model from the MNI template brain, but for the entire intracranial volume and not just the brain. My original plan was to extract the brain (or use the provided brain mask) and then use that brain mask for segmentation. While this works great, I'm missing quite a bit of the intracranial space (particularly the CSF regions at the periphery of the brain). The options I'm weighing now are to 1) manually adjust the brain mask to encompass the whole volume or 2) run the segmentation for the whole head (not just the brain mask), but I'm not sure if that would work. \r\n\r\nAfter this, my goal is to take a subject MRI, extract the brain from that MRI (in the same manner as MNI, so I get the whole intracranial volume), and then register it to the MNI brain. That way, I can take the MNI segmentation and warp it to the subject brain. \r\n\r\nThe other challenge that I foresee is that as far as I am aware, the segmentation priors used in ANTs do not include anything outside of the brain. So even if I can extract the whole intracranial space, would I be able to segment the CSF outside of the periphery of the brain? Or am I wrong, here?\r\n\r\nDoes anyone have any advice? I'm new to ANTs so any help would be much appreciated.\r\n\r\nThanks,\r\nSebastian "},"comment":{"url":"https://api.github.com/repos/ANTsX/ANTs/issues/comments/436360385","html_url":"https://github.com/ANTsX/ANTs/issues/625#issuecomment-436360385","issue_url":"https://api.github.com/repos/ANTsX/ANTs/issues/625","id":436360385,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNjM2MDM4NQ==","user":{"login":"jsebgiudice","id":42451197,"node_id":"MDQ6VXNlcjQyNDUxMTk3","avatar_url":"https://avatars1.githubusercontent.com/u/42451197?v=4","gravatar_id":"","url":"https://api.github.com/users/jsebgiudice","html_url":"https://github.com/jsebgiudice","followers_url":"https://api.github.com/users/jsebgiudice/followers","following_url":"https://api.github.com/users/jsebgiudice/following{/other_user}","gists_url":"https://api.github.com/users/jsebgiudice/gists{/gist_id}","starred_url":"https://api.github.com/users/jsebgiudice/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsebgiudice/subscriptions","organizations_url":"https://api.github.com/users/jsebgiudice/orgs","repos_url":"https://api.github.com/users/jsebgiudice/repos","events_url":"https://api.github.com/users/jsebgiudice/events{/privacy}","received_events_url":"https://api.github.com/users/jsebgiudice/received_events","type":"User","site_admin":false},"created_at":"2018-11-06T18:36:06Z","updated_at":"2018-11-06T18:36:06Z","author_association":"NONE","body":"Hi Gabriel,\r\n\r\nThanks for commenting. That sounds promising, although the only problem is that in my application, I actually need the brain mask for my analyses, which involves creating 3D models from the mask. However, now that you mention it, doing it through and affine registration from the template to subject might be a good way of doing this. Do you find that the affine transformation has enough \"information\" to accurately map one skull to another? \r\n\r\nAlso, since you're looking at brain volume, and specifically relative to MNI, have you found that the MNI brain is unrealistically large? Just the brain volume alone (not ICV, just from regular extraction) is around 1800 cm3 and published averages are in the 1300-1500 cm3 ball park. It's not just MNI either, Colin27 has a very above-average volume and there doesnt seem to be any explanation in the literature for this... "}}
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