{"action":"created","issue":{"url":"https://api.github.com/repos/mne-tools/mne-python/issues/2555","labels_url":"https://api.github.com/repos/mne-tools/mne-python/issues/2555/labels{/name}","comments_url":"https://api.github.com/repos/mne-tools/mne-python/issues/2555/comments","events_url":"https://api.github.com/repos/mne-tools/mne-python/issues/2555/events","html_url":"https://github.com/mne-tools/mne-python/issues/2555","id":113116085,"number":2555,"title":"Visualizing brains in 3-D space?","user":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-23T23:25:11Z","updated_at":"2015-10-25T21:17:12Z","closed_at":null,"body":"I'm trying to figure out if it's feasible to visualize brains in 3-D space with python. I know there's a lot of software out there (e.g., freesurfer/pysurfer, or pycortex) that lets you do this with solid MR scans, but in my case I basically just have a Nifty file with pretty low-quality scans.\r\n\r\nIs there any way in MNE (or python more generally) to just load a Nifty file of someone's brain reconstruction, a 3-D array of numbers denoting electrode positions, and then make scatterplots etc on top?"},"comment":{"url":"https://api.github.com/repos/mne-tools/mne-python/issues/comments/150970142","html_url":"https://github.com/mne-tools/mne-python/issues/2555#issuecomment-150970142","issue_url":"https://api.github.com/repos/mne-tools/mne-python/issues/2555","id":150970142,"user":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"created_at":"2015-10-25T21:17:12Z","updated_at":"2015-10-25T21:17:12Z","body":"That looks useful - thanks for the tip. I basically want to do things like\nwhat you just linked to, only on a 3D brain w/ some orientation. There are\na few packages that do this in matlab but I'm hoping something exists in\npython for this. Unfortunately the ECoG world is mostly a matlab world :P\n\nOn Sun, Oct 25, 2015 at 2:04 PM, Alexandre Gramfort <\nnotifications@github.com> wrote:\n\n> the best way to visualize brain slices is with nilearn AFAIK.\n>\n> we use it in\n>\n> http://martinos.org/mne/dev/auto_examples/inverse/plot_lcmv_beamformer_volume.html#sphx-glr-auto-examples-inverse-plot-lcmv-beamformer-volume-py\n>\n> if you need more you'll need to code a bit.\n>\n>\n> On Sat, Oct 24, 2015 at 1:25 AM, Chris Holdgraf <notifications@github.com>\n> wrote:\n>\n> > I'm trying to figure out if it's feasible to visualize brains in 3-D\n> space\n> > with python. I know there's a lot of software out there (e.g.,\n> > freesurfer/pysurfer, or pycortex) that lets you do this with solid MR\n> > scans, but in my case I basically just have a Nifty file with pretty\n> > low-quality scans.\n> >\n> > Is there any way in MNE (or python more generally) to just load a Nifty\n> > file of someone's brain reconstruction, a 3-D array of numbers denoting\n> > electrode positions, and then make scatterplots etc on top?\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/mne-tools/mne-python/issues/2555>.\n> >\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/mne-tools/mne-python/issues/2555#issuecomment-150969067>\n> .\n>\n"}}