{"action":"opened","issue":{"url":"https://api.github.com/repos/BIC-MNI/mni_autoreg/issues/11","labels_url":"https://api.github.com/repos/BIC-MNI/mni_autoreg/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/BIC-MNI/mni_autoreg/issues/11/comments","events_url":"https://api.github.com/repos/BIC-MNI/mni_autoreg/issues/11/events","html_url":"https://github.com/BIC-MNI/mni_autoreg/issues/11","id":101686744,"number":11,"title":"mincblur -3dfwhm dimension order mismatch","user":{"login":"mcvaneede","id":808403,"avatar_url":"https://avatars.githubusercontent.com/u/808403?v=3","gravatar_id":"","url":"https://api.github.com/users/mcvaneede","html_url":"https://github.com/mcvaneede","followers_url":"https://api.github.com/users/mcvaneede/followers","following_url":"https://api.github.com/users/mcvaneede/following{/other_user}","gists_url":"https://api.github.com/users/mcvaneede/gists{/gist_id}","starred_url":"https://api.github.com/users/mcvaneede/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcvaneede/subscriptions","organizations_url":"https://api.github.com/users/mcvaneede/orgs","repos_url":"https://api.github.com/users/mcvaneede/repos","events_url":"https://api.github.com/users/mcvaneede/events{/privacy}","received_events_url":"https://api.github.com/users/mcvaneede/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-18T15:45:52Z","updated_at":"2015-08-18T15:45:52Z","closed_at":null,"body":"I was trying to apply a 3D Gaussian blurring kernel to a 2D slice:\r\n\r\n```\r\nmincinfo 2D_slice.mnc \r\nfile: 2D_slice.mnc\r\nimage: unsigned short 0 to 65535\r\nimage dimensions: zspace xspace yspace\r\n    dimension name         length         step        start\r\n    --------------         ------         ----        -----\r\n    zspace                      1         0.38        -0.38\r\n    xspace                    192    -0.260417      24.8698\r\n    yspace                    200        -0.25       24.875\r\n```\r\n\r\nReading the manual page for mincblur, it seems like it wants the size of the kernel in x,y,z order (not dimension order), however the following command:\r\n\r\n```\r\nmincblur  -3dfwhm 5.0 5.0 0.0001 2D_slice.mnc 2D_slice_5mm_xy\r\nMaking byte volume...\r\n```\r\n\r\nUpon visual inspection does not actually blur in the x-dimension. So I tried to feed the arguments in dimension order, but got:\r\n\r\n```\r\nmincblur  -3dfwhm 0.0001 5.0 5.0  2D_slice.mnc 2D_slice_5mm_xy\r\nError in mincblur in file /projects/mice/share/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/src/minc-toolkit/mni_autoreg/mincblur/apodize_data.c, line 91\r\nFWHM is greater than slice dimension\r\n```\r\n\r\nI then made the slice artificially thick and tried the last command again. This correctly blurred the file in x and y. It looks like mincblur determines whether the blur can be applied based on the x,y,z input, but applies it to the dimension order that the file is stored in:\r\n\r\n```\r\nminc_modify_header -dinsert zspace:step=10 2D_slice.mnc\r\nmincblur  -3dfwhm 0.0001  5.0 5.0  2D_slice.mnc 2D_slice_5mm_xy\r\nMaking byte volume...\r\n```\r\n"}}