{"action":"closed","issue":{"url":"https://api.github.com/repos/binarybottle/mindboggle/issues/55","labels_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/55/labels{/name}","comments_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/55/comments","events_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/55/events","html_url":"https://github.com/binarybottle/mindboggle/issues/55","id":94573946,"number":55,"title":"Regions used in mindboggle","user":{"login":"cMadan","id":6385051,"avatar_url":"https://avatars.githubusercontent.com/u/6385051?v=3","gravatar_id":"","url":"https://api.github.com/users/cMadan","html_url":"https://github.com/cMadan","followers_url":"https://api.github.com/users/cMadan/followers","following_url":"https://api.github.com/users/cMadan/following{/other_user}","gists_url":"https://api.github.com/users/cMadan/gists{/gist_id}","starred_url":"https://api.github.com/users/cMadan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cMadan/subscriptions","organizations_url":"https://api.github.com/users/cMadan/orgs","repos_url":"https://api.github.com/users/cMadan/repos","events_url":"https://api.github.com/users/cMadan/events{/privacy}","received_events_url":"https://api.github.com/users/cMadan/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-07-12T15:33:46Z","updated_at":"2015-07-13T08:04:25Z","closed_at":"2015-07-13T08:04:25Z","body":"In the FAQ (http://www.mindboggle.info/faq/labels.html), there is some rationale outlined for combining some of the regions that are delineated in the DKT atlas, e.g., combining the three inferior frontal regions into a single region. However, in the example mindboggle output, it appears that the three regions are not combined (e.g., thickinthehead_per_freesurfer_cortex_label.csv). I can see that it is currently an open question of which is better, i.e., 31 or 25 cortical regions (https://neurostars.org/p/2680/). However, that post does indicate that mindboggle currently outputs 25 regions.\r\n\r\nIs this an discrepancy in the current output vs. FAQ due to a change to using 31 regions instead? Perhaps a solution to this would be to default to one set of regions (31 vs. 25), but allow the user to specify if they want the other as a flag when running mindboggle? In either case, the FAQ should be updated to match the current output of mindboggle.\r\n\r\nPart of my interest in using mindboggle was to see how cortical thickness estimates would look in the DKT-25 protocol, so I wanted to see an example output that included both sets (i.e., FreeSurfer would use the 31 regions still, mindboggle would provide the 25 regions, calculated from the same participant."}}