{"action":"created","issue":{"url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/310","repository_url":"https://api.github.com/repos/BRAINSia/BRAINSTools","labels_url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/310/labels{/name}","comments_url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/310/comments","events_url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/310/events","html_url":"https://github.com/BRAINSia/BRAINSTools/issues/310","id":190437430,"number":310,"title":"error in NIFTItoNRRD handling of space directions","user":{"login":"vmagnotta","id":322541,"avatar_url":"https://avatars.githubusercontent.com/u/322541?v=3","gravatar_id":"","url":"https://api.github.com/users/vmagnotta","html_url":"https://github.com/vmagnotta","followers_url":"https://api.github.com/users/vmagnotta/followers","following_url":"https://api.github.com/users/vmagnotta/following{/other_user}","gists_url":"https://api.github.com/users/vmagnotta/gists{/gist_id}","starred_url":"https://api.github.com/users/vmagnotta/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vmagnotta/subscriptions","organizations_url":"https://api.github.com/users/vmagnotta/orgs","repos_url":"https://api.github.com/users/vmagnotta/repos","events_url":"https://api.github.com/users/vmagnotta/events{/privacy}","received_events_url":"https://api.github.com/users/vmagnotta/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-11-18T22:29:51Z","updated_at":"2016-11-20T14:27:03Z","closed_at":null,"body":"There seems to be an issue with the proper handling of image orientation in DWIConvert. If a DICOM series is directly converted to NiFTI versus the conversion from DICOM->NRRD->NIFTI the NIFTI sform matrix is not consistent while the qform matrix is. Slicer shows the image in the same orientation likely because it is using the qform orientation. \r\n\r\nThe problem is related to the srow_z rotation portion of the transform which is getting multiplied by -1.  The translation part of the matrix is correct."},"comment":{"url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/comments/261781426","html_url":"https://github.com/BRAINSia/BRAINSTools/issues/310#issuecomment-261781426","issue_url":"https://api.github.com/repos/BRAINSia/BRAINSTools/issues/310","id":261781426,"user":{"login":"hjmjohnson","id":313970,"avatar_url":"https://avatars.githubusercontent.com/u/313970?v=3","gravatar_id":"","url":"https://api.github.com/users/hjmjohnson","html_url":"https://github.com/hjmjohnson","followers_url":"https://api.github.com/users/hjmjohnson/followers","following_url":"https://api.github.com/users/hjmjohnson/following{/other_user}","gists_url":"https://api.github.com/users/hjmjohnson/gists{/gist_id}","starred_url":"https://api.github.com/users/hjmjohnson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjmjohnson/subscriptions","organizations_url":"https://api.github.com/users/hjmjohnson/orgs","repos_url":"https://api.github.com/users/hjmjohnson/repos","events_url":"https://api.github.com/users/hjmjohnson/events{/privacy}","received_events_url":"https://api.github.com/users/hjmjohnson/received_events","type":"User","site_admin":false},"created_at":"2016-11-20T14:27:03Z","updated_at":"2016-11-20T14:27:03Z","body":"Vince,\n\n \n\nI am working through several issues with properly representing Nrrd files and Nifti files from DWIConvert.\n\n \n\n \n\nAnother popular tool for many dwi processing to convert dicom to NIFTI is the dcm2niix tool.   I’ve previously had conversations with the author of that tool, and I thought we had resolved the interpretation issues.\n\n \n\nhttps://github.com/rordenlab/dcm2niix/issues/40\n\n \n\nThis is a discussion about some data that I am working with that is from BC Ho’s study.\n\n \n\nCould you please comment if you think the comments are correct, or if you think that perhaps there is a mis-interpretation of the data that I sent?\n\n \n\nThanks,\n\nHans\n\n \n\n \n\n-- \n\n \n\n \n\nFrom: \"Vincent A. Magnotta\" <notifications@github.com>\nReply-To: BRAINSia/BRAINSTools <reply@reply.github.com>\nDate: Saturday, November 19, 2016 at 9:03 PM\nTo: BRAINSia/BRAINSTools <BRAINSTools@noreply.github.com>\nCc: Hans Johnson <hans.j.johnson@gmail.com>, Comment <comment@noreply.github.com>\nSubject: Re: [BRAINSia/BRAINSTools] error in NIFTItoNRRD handling of space directions (#310)\n\n \n\nHans\n\nThat may be the case. It is odd that the sform is wrong while the qform is correct.\n\nVince\n\n---\nAssociate Professor\nDepartment of Radiology\nL311 PBDB\n169 Newton Road\nIowa City, IA 52242\nE-mail: vincent-magnotta@uiowa.edu<mailto:vincent-magnotta@uiowa.edu>\nPhone: 319-335-5482 Fax: 319-353-6275\nWebsite: http://www.healthcare.uiowa.edu/Radiology\n\nOn Nov 19, 2016, at 8:07 PM, Hans Johnson <notifications@github.com<mailto:notifications@github.com>> wrote:\n\nThanks Vince. I’ll need to look into this again. I thought that if the qform is set, then the sform is NOT set, and is not used.\n\n\n\nHans\n\n\n\n\n\n--\n\n\n\n\n\nFrom: \"Vincent A. Magnotta\" <notifications@github.com<mailto:notifications@github.com>>\nReply-To: BRAINSia/BRAINSTools <reply@reply.github.com<mailto:reply@reply.github.com>>\nDate: Saturday, November 19, 2016 at 6:29 PM\nTo: BRAINSia/BRAINSTools <BRAINSTools@noreply.github.com<mailto:BRAINSTools@noreply.github.com>>\nCc: Hans Johnson <hans.j.johnson@gmail.com<mailto:hans.j.johnson@gmail.com>>, Comment <comment@noreply.github.com<mailto:comment@noreply.github.com>>\nSubject: Re: [BRAINSia/BRAINSTools] error in NIFTItoNRRD handling of space directions (#310)\n\n\n\nHans,\n\nI looked at this some on Friday. Since both transforms originate from the image direction matrix, it would assume the bug could be in the helper function that generates the sform matrix from the direction cosines.\n\nVince\n\n\n--\nAssociate Professor\nDepartment of Radiology\nL311 PBDB\n169 Newton Road\nIowa City, IA 52242\nE-mail: vincent-magnotta@uiowa.edu<mailto:vincent-magnotta@uiowa.edu>\nPhone: 319-335-5482 Fax: 319-353-6275\nWebsite: http://www.healthcare.uiowa.edu/Radiology\n\nFrom: Hans Johnson <notifications@github.com<mailto:notifications@github.com>>\nReply-To: BRAINSia/BRAINSTools <reply@reply.github.com<mailto:reply@reply.github.com>>\nDate: Saturday, November 19, 2016 at 5:48 PM\nTo: BRAINSia/BRAINSTools <BRAINSTools@noreply.github.com<mailto:BRAINSTools@noreply.github.com>>\nCc: Vincent Magnotta <vincent-magnotta@uiowa.edu<mailto:vincent-magnotta@uiowa.edu>>, Mention <mention@noreply.github.com<mailto:mention@noreply.github.com>>\nSubject: Re: [BRAINSia/BRAINSTools] error in NIFTItoNRRD handling of space directions (#310)\n\n\n@vmagnotta<https://github.com/vmagnotta> Vince, I'm looking at this code now. Do you happen to know where in the code the problem is occurring?\n\n—\nYou are receiving this because you were mentioned.\nReply to this email directly, view it on GitHub<https://github.com/BRAINSia/BRAINSTools/issues/310#issuecomment-261747873>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AATr7foibZiSqXmc553brw1K8r5mUwHjks5q_4rfgaJpZM4K2_j->.\n\n\n________________________________\nNotice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. 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