{"action":"created","issue":{"url":"https://api.github.com/repos/vistalab/vistasoft/issues/148","labels_url":"https://api.github.com/repos/vistalab/vistasoft/issues/148/labels{/name}","comments_url":"https://api.github.com/repos/vistalab/vistasoft/issues/148/comments","events_url":"https://api.github.com/repos/vistalab/vistasoft/issues/148/events","html_url":"https://github.com/vistalab/vistasoft/issues/148","id":121131114,"number":148,"title":"Quick question regarding xform in dtiRawBuildBvecs.m","user":{"login":"shrimpj","id":16172014,"avatar_url":"https://avatars.githubusercontent.com/u/16172014?v=3","gravatar_id":"","url":"https://api.github.com/users/shrimpj","html_url":"https://github.com/shrimpj","followers_url":"https://api.github.com/users/shrimpj/followers","following_url":"https://api.github.com/users/shrimpj/following{/other_user}","gists_url":"https://api.github.com/users/shrimpj/gists{/gist_id}","starred_url":"https://api.github.com/users/shrimpj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shrimpj/subscriptions","organizations_url":"https://api.github.com/users/shrimpj/orgs","repos_url":"https://api.github.com/users/shrimpj/repos","events_url":"https://api.github.com/users/shrimpj/events{/privacy}","received_events_url":"https://api.github.com/users/shrimpj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-12-09T00:14:04Z","updated_at":"2015-12-09T02:38:43Z","closed_at":null,"body":"Hi all,\r\n\r\nI used freesurfer command mri_info to get xform information as I told by our radiographer. https://surfer.nmr.mgh.harvard.edu/fswiki/mri_info. He told me the only transformation he did was to flipped y axial when he converted raw DTI data to Nifti files. I assume this is the process of converting image from scanner coordinate to anatomical imaging coordinate.\r\n\r\nI wonder which on should I use xforminfo or voxle to ras transformation matrix for this function? Because two of them are different.\r\n   xform info: x_r =  -0.9974, y_r =  -0.0561, z_r =  -0.0462, c_r =    -0.5960\r\n              \r\n              : x_a =  -0.0578, y_a =   0.9977, z_a =   0.0364, c_a =    -9.5551\r\n              \r\n              : x_s =  -0.0441, y_s =  -0.0390, z_s =   0.9983, c_s =    10.5253\r\n\r\n  voxel to ras transform:\r\n                                 -1.7142  -0.0964  -0.2315   117.4822\r\n               \r\n                                 -0.0993   1.7147   0.1823  -114.6716\r\n               \r\n                                 -0.0757  -0.0670   4.9992   -27.8324\r\n                \r\n                                  0.0000   0.0000   0.0000     1.0000\r\nAny suggestions would be grateful!\r\n\r\nBW,\r\nJoyce"},"comment":{"url":"https://api.github.com/repos/vistalab/vistasoft/issues/comments/163088108","html_url":"https://github.com/vistalab/vistasoft/issues/148#issuecomment-163088108","issue_url":"https://api.github.com/repos/vistalab/vistasoft/issues/148","id":163088108,"user":{"login":"shrimpj","id":16172014,"avatar_url":"https://avatars.githubusercontent.com/u/16172014?v=3","gravatar_id":"","url":"https://api.github.com/users/shrimpj","html_url":"https://github.com/shrimpj","followers_url":"https://api.github.com/users/shrimpj/followers","following_url":"https://api.github.com/users/shrimpj/following{/other_user}","gists_url":"https://api.github.com/users/shrimpj/gists{/gist_id}","starred_url":"https://api.github.com/users/shrimpj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shrimpj/subscriptions","organizations_url":"https://api.github.com/users/shrimpj/orgs","repos_url":"https://api.github.com/users/shrimpj/repos","events_url":"https://api.github.com/users/shrimpj/events{/privacy}","received_events_url":"https://api.github.com/users/shrimpj/received_events","type":"User","site_admin":false},"created_at":"2015-12-09T02:38:43Z","updated_at":"2015-12-09T02:38:43Z","body":"Thanks you so much for your reply! I tried all of them including xform=eye(3) as it 's given by the example. Why did you use eye(4)? I did not use the last column as I think it's irrelevant.\n\nJoyce \n\n\n> On Dec 8, 2015, at 17:29, Bob Dougherty <notifications@github.com> wrote:\n> \n> No, I'm not familiar with idot files. You may just need to try different xforms to see what works. I'd start with no xform (i.e., eye(4)).\n> \n> —\n> Reply to this email directly or view it on GitHub.\n> \n"}}