{"action":"created","issue":{"url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/163","repository_url":"https://api.github.com/repos/rordenlab/dcm2niix","labels_url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/163/labels{/name}","comments_url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/163/comments","events_url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/163/events","html_url":"https://github.com/rordenlab/dcm2niix/issues/163","id":298249553,"number":163,"title":"Suggestions for GE dicom header info to use in BIDS sidecar ","user":{"login":"mick-d","id":4580257,"avatar_url":"https://avatars3.githubusercontent.com/u/4580257?v=4","gravatar_id":"","url":"https://api.github.com/users/mick-d","html_url":"https://github.com/mick-d","followers_url":"https://api.github.com/users/mick-d/followers","following_url":"https://api.github.com/users/mick-d/following{/other_user}","gists_url":"https://api.github.com/users/mick-d/gists{/gist_id}","starred_url":"https://api.github.com/users/mick-d/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mick-d/subscriptions","organizations_url":"https://api.github.com/users/mick-d/orgs","repos_url":"https://api.github.com/users/mick-d/repos","events_url":"https://api.github.com/users/mick-d/events{/privacy}","received_events_url":"https://api.github.com/users/mick-d/received_events","type":"User","site_admin":false},"labels":[{"id":139333300,"url":"https://api.github.com/repos/rordenlab/dcm2niix/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":25,"created_at":"2018-02-19T11:55:34Z","updated_at":"2018-04-12T14:30:52Z","closed_at":"2018-04-10T16:33:35Z","author_association":"NONE","body":"Hi,\r\n\r\nI needed to use the BIDS sidecar created by dcm2niix for one project, and unfortunately some information about DICOM data from a GE Signa (HDxt) scanner was missing. I am opening an issue here as recommended by Chris Gorgolewski on this [NeuroStars post](https://neurostars.org/t/getting-missing-ge-information-required-by-bids-for-common-preprocessing/1357/2?u=michael) to provide information which might be useful for the missing information I could find and the missing information I could not solve. Please find the original post below for convenience.\r\n\r\nI could not get any of the following fields (among others) with dcm2niix (including latest version I compiled myself at the time of writing):\r\n* “_BandwidthPerPixelPhaseEncode_”\r\n* “_EffectiveEchoSpacing_”\r\n* “_TotalReadoutTime_”\r\n* “_SliceTiming_”\r\n* “_PhaseEncodingDirection_”\r\n\r\nI could manually get _EffectiveEchoSpacing_ by looking at DICOM field 0043 102c (cf [GE doc](https://wiki.cancerimagingarchive.net/download/attachments/3539047/GE-Signa-MR.pdf?version=1&modificationDate=1357067930098)) and _SliceTiming_ by looking at DICOM field “Trigger Time”.\r\n\r\nI could compute _TotalReadoutTime_ with (<DICOM field “IMG Columns”> - 1) * (1 / _EffectiveEchoSpacing_).\r\n\r\nHowever I could not find a way to get _BandwidthPerPixelPhaseEncode_ (the DICOM field “ACQ Pixel Bandwidth” seems to be something different) and could only get part of the _PhaseEncodingDirection_: the direction but not the sign (direction was “j” as DICOM field “ACQ Phase Encoding Direction” was ROW).\r\n"},"comment":{"url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/comments/380826006","html_url":"https://github.com/rordenlab/dcm2niix/issues/163#issuecomment-380826006","issue_url":"https://api.github.com/repos/rordenlab/dcm2niix/issues/163","id":380826006,"user":{"login":"xiangruili","id":19894855,"avatar_url":"https://avatars3.githubusercontent.com/u/19894855?v=4","gravatar_id":"","url":"https://api.github.com/users/xiangruili","html_url":"https://github.com/xiangruili","followers_url":"https://api.github.com/users/xiangruili/followers","following_url":"https://api.github.com/users/xiangruili/following{/other_user}","gists_url":"https://api.github.com/users/xiangruili/gists{/gist_id}","starred_url":"https://api.github.com/users/xiangruili/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xiangruili/subscriptions","organizations_url":"https://api.github.com/users/xiangruili/orgs","repos_url":"https://api.github.com/users/xiangruili/repos","events_url":"https://api.github.com/users/xiangruili/events{/privacy}","received_events_url":"https://api.github.com/users/xiangruili/received_events","type":"User","site_admin":false},"created_at":"2018-04-12T14:30:52Z","updated_at":"2018-04-12T14:30:52Z","author_association":"NONE","body":"Thanks for the testing images.\r\n\r\nI compared all the dicom tags for following two series:\r\nAxial_rsfMRI_multiphase_EPI\r\nAxial_rsfMRI_multiphase_EPI_reverse_blip\r\n\r\nI believe I have narrowed down the possible difference (which could related to \"reverse_blip\") to the following tag:\r\n(0043,102A) 'OB' 'UserDefineData'. \r\nUnfortunately, it is not human-readable. \r\n\r\nI am not a GE guy. I know, if we have a dicom file for Siemens, the scanner can import the sequence from the dicom file. Is this true for GE? In other words, can GE system import correct \"blip\" info from the above two dicom files? If so, we can try to decode \"UserDefineData\". Otherwise I think it is end of the game for this purpose.\r\n_____________\r\nXiangrui Li, Ph.D.\r\nCenter for Cognitive and Behavioral Brain Imaging\r\nThe Ohio State University\r\nPhone: 614-292-1847\r\n\r\nFrom: john lee\r\nDate: 2018-04-12 09:18\r\nTo: rordenlab/dcm2niix\r\nCC: xiangruili; Mention\r\nSubject: Re: [rordenlab/dcm2niix] Suggestions for GE dicom header info to use in BIDS sidecar (#163)\r\nThanks again for all the help with this. It is disappointing that so many sequences from GE have this issue.\r\nI'm sharing a full session collected by @roopchansinghv with more informative series descriptions. Hopefully this helps in the future if any further testing is required, or perhaps other GE issues. It contains GE product DTI (forward and reverse blip), multiphase EPI (forward and reversed blip), and epiRT (forward and reversed blip). As determined above, phase encoding direction should only be inferred in the last case (with epiRT).\r\nhttps://drive.google.com/file/d/12KRejaoQ1FyidUQAhPze9DGawJYZqFbs/view?usp=sharing\r\n—\r\nYou are receiving this because you were mentioned.\r\nReply to this email directly, view it on GitHub, or mute the thread."}}
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