{"action":"created","issue":{"url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/40","repository_url":"https://api.github.com/repos/neurolabusc/dcm2niix","labels_url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/40/comments","events_url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/40/events","html_url":"https://github.com/neurolabusc/dcm2niix/issues/40","id":172160904,"number":40,"title":"Incorrect conversion of DWI data","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-08-19T15:43:47Z","updated_at":"2016-08-20T08:12:07Z","closed_at":null,"body":"Chris,\r\n\r\nI am working to convert data into the BIDS format, but using the dcm2niix tool is resulting in the following warnings:\r\n\r\n /scratch/johnsonhj/local/bin/dcm2niix   -f sub-aaa_ses-001_dwi  -b   -z   -o $(pwd)/output   ${DICOM_DIR}\r\n\r\nChris Rorden's dcm2niiX version 15Aug2016 (64-bit)\r\nWARNING: CSA 'ProtocolSliceNumber' SUGGESTS REVERSED SLICE ORDER: SPATIAL AND DTI COORDINATES UNTESTED\r\n\r\nThe generated json file is:\r\n{\r\n\t\"Manufacturer\": \"Siemens\",\r\n\t\"ManufacturersModelName\": \"TrioTim\",\r\n\t\"MagneticFieldStrength\": 3,\r\n\t\"FlipAngle\": 90,\r\n\t\"EchoTime\": 0.088,\r\n\t\"RepetitionTime\": 9.1,\r\n\t\"EffectiveEchoSpacing\": 0.000400005,\r\n\t\"SliceTiming\": [\r\n\t\t4.4375,\r\n\t\t9.0075,\r\n\t\t4.3075,\r\n\t\t8.875,\r\n\t\t4.1775,\r\n\t\t8.745,\r\n\t\t4.0475,\r\n\t\t8.615,\r\n\t\t3.9175,\r\n\t\t8.485,\r\n\t\t3.785,\r\n\t\t8.355,\r\n\t\t3.655,\r\n\t\t8.2225,\r\n\t\t3.525,\r\n\t\t8.0925,\r\n\t\t3.395,\r\n\t\t7.9625,\r\n\t\t3.265,\r\n\t\t7.8325,\r\n\t\t3.1325,\r\n\t\t7.7,\r\n\t\t3.0025,\r\n\t\t7.57,\r\n\t\t2.8725,\r\n\t\t7.44,\r\n\t\t2.7425,\r\n\t\t7.31,\r\n\t\t2.6125,\r\n\t\t7.18,\r\n\t\t2.48,\r\n\t\t7.0475,\r\n\t\t2.35,\r\n\t\t6.9175,\r\n\t\t2.22,\r\n\t\t6.7875,\r\n\t\t2.09,\r\n\t\t6.6575,\r\n\t\t1.9575,\r\n\t\t6.5275,\r\n\t\t1.8275,\r\n\t\t6.395,\r\n\t\t1.6975,\r\n\t\t6.265,\r\n\t\t1.5675,\r\n\t\t6.135,\r\n\t\t1.4375,\r\n\t\t6.005,\r\n\t\t1.305,\r\n\t\t5.875,\r\n\t\t1.175,\r\n\t\t5.7425,\r\n\t\t1.045,\r\n\t\t5.6125,\r\n\t\t0.915,\r\n\t\t5.4825,\r\n\t\t0.785,\r\n\t\t5.3525,\r\n\t\t0.6525,\r\n\t\t5.2225,\r\n\t\t0.5225,\r\n\t\t5.09,\r\n\t\t0.3925,\r\n\t\t4.96,\r\n\t\t0.2625,\r\n\t\t4.83,\r\n\t\t0.1325,\r\n\t\t4.7,\r\n\t\t0,\r\n\t\t4.57\t],\r\n\t\"PhaseEncodingDirection\": \"j-\"\r\n}\r\n\r\n\r\n\r\nIs this something that I should be worried about?\r\n\r\nAdditionally, when I load this into the Slicer application, the images always are incorrectly oriented.\r\n\r\nAny advice would be greatly appreciated.\r\n\r\nThanks,\r\nHans\r\n"},"comment":{"url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/comments/241186539","html_url":"https://github.com/neurolabusc/dcm2niix/issues/40#issuecomment-241186539","issue_url":"https://api.github.com/repos/neurolabusc/dcm2niix/issues/40","id":241186539,"user":{"login":"neurolabusc","id":8930807,"avatar_url":"https://avatars.githubusercontent.com/u/8930807?v=3","gravatar_id":"","url":"https://api.github.com/users/neurolabusc","html_url":"https://github.com/neurolabusc","followers_url":"https://api.github.com/users/neurolabusc/followers","following_url":"https://api.github.com/users/neurolabusc/following{/other_user}","gists_url":"https://api.github.com/users/neurolabusc/gists{/gist_id}","starred_url":"https://api.github.com/users/neurolabusc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/neurolabusc/subscriptions","organizations_url":"https://api.github.com/users/neurolabusc/orgs","repos_url":"https://api.github.com/users/neurolabusc/repos","events_url":"https://api.github.com/users/neurolabusc/events{/privacy}","received_events_url":"https://api.github.com/users/neurolabusc/received_events","type":"User","site_admin":false},"created_at":"2016-08-20T08:12:07Z","updated_at":"2016-08-20T08:12:07Z","body":"Hans,\r\n 1.) The TE, TR, and slice timings all look plausible. The thing causes my software to generate a warning is the order of the slice timing reported in the Siemens CSA headers' \"MosaicRefAcqTimes\" tag. Specifically, all the Siemens and CMRR sequences I have used generate one of three slice orders: ascending, descending, and interleaved ascending. However, your CSA header suggests that the data was acquired as INTERLEAVED DESCENDING. Since this order was not available on any of our systems, it was not included in our validation dataset\r\n https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging\r\n 2.) Can you provide specifics describing why the BIDS data is incorrect? Are the TE/TR/Slice Order not what was requested on the console? Again, to my eye they all look plausible, but the slice order is highly unusual. Is this a Siemens product, CMRR sequence or something else? What version Siemens software are you using (with TrioTim I would expect B17 or B19 for US users)?\r\n 3.) I do note that the TR and TE are reported in SECONDS as required by BIDS (http://bids.neuroimaging.io/bids_spec1.0.0-rc2.pdf), but the SliceTIming are in Milliseconds. I will drop ChrisG a line on whether this should be changed.\r\n 4.) I would strongly suggest you do the validation I suggest in the Word document at\r\n  http://people.cas.sc.edu/rorden/mricron/dcm2nii.html\r\nThe trick is that the Siemens DICOM files report gradients with respect to the scanner, while neuroimaging tools require them reported with respect to the imaging plane.\r\n 5.) I would be happy to look at a dataset, send me an email with a link to a sample DICOM dataset as well as the PDF export of the sequence.\r\n\r\n-c\r\n"}}
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