{"action":"closed","issue":{"url":"https://api.github.com/repos/stnava/ANTs/issues/178","labels_url":"https://api.github.com/repos/stnava/ANTs/issues/178/labels{/name}","comments_url":"https://api.github.com/repos/stnava/ANTs/issues/178/comments","events_url":"https://api.github.com/repos/stnava/ANTs/issues/178/events","html_url":"https://github.com/stnava/ANTs/issues/178","id":68127065,"number":178,"title":"Normalization of brain images with inflated ventricles","user":{"login":"dicaincadi","id":11926613,"avatar_url":"https://avatars.githubusercontent.com/u/11926613?v=3","gravatar_id":"","url":"https://api.github.com/users/dicaincadi","html_url":"https://github.com/dicaincadi","followers_url":"https://api.github.com/users/dicaincadi/followers","following_url":"https://api.github.com/users/dicaincadi/following{/other_user}","gists_url":"https://api.github.com/users/dicaincadi/gists{/gist_id}","starred_url":"https://api.github.com/users/dicaincadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dicaincadi/subscriptions","organizations_url":"https://api.github.com/users/dicaincadi/orgs","repos_url":"https://api.github.com/users/dicaincadi/repos","events_url":"https://api.github.com/users/dicaincadi/events{/privacy}","received_events_url":"https://api.github.com/users/dicaincadi/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-04-13T15:32:03Z","updated_at":"2015-04-15T13:49:54Z","closed_at":"2015-04-15T13:49:54Z","body":"High experts,\r\n\r\nWe are performing ANTS transformation of T1-weighted brain MRI from subject space to standard MNI space. While checking the transformation, in the back projection, we observe that gray matter tissue has moved into the ventricles (see attached snapshots)\r\n\r\n![screen shot 2015-04-08 at 14 18 29](https://cloud.githubusercontent.com/assets/11926613/7118962/8d2fc9cc-e1d0-11e4-9244-ddfc60ec94af.png)\r\n\r\nThe diffeomorphic mapping employed was SyN and affine transformation. We have employed either CC or MI as fitness metric, and we have varied the radius, obtaining a better result with larger radius (>5). However we always have issues within the ventricles.\r\n\r\nWhat would you reccomend us to face this?\r\nThis is the code line we were employing.\r\nANTS 3 -m CC[$templateName,$movingIM,1,7] -t SyN[0.25] -r Gauss[3,0] -o $normAnatOutDir/T1_fov_denoised -i 100x100x100x30 --use-Histogram-Matching  --number-of-affine-iterations 10000x10000x10000\r\n\r\nAny advide will be really appreciated.\r\n\r\nThanks\r\n\r\nJosé"}}