Use the DICOM viewer I mentioned earlier and the specified field. Matt.
From: Marc Dubin <[email protected]<mailto:[email protected]>> Date: Saturday, July 21, 2018 at 11:13 PM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input Thanks…..for some reason DwellTime isn’t listed in my json files (attached). On 21 Jul 2018, at 23:59, Harms, Michael wrote: Hi, Use a DICOM reader to check the value of (0019,1018). Or, IIRC, the value is extracted as “DwellTime” in the BIDS json returned by ‘dcm2niix’. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: Marc Dubin <[email protected]<mailto:[email protected]>> Date: Saturday, July 21, 2018 at 10:28 PM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input Hi Matt, Do you know how to find the following? I was unable to find them in the dcm2niix json file or in the Matlab metadata structure. I just want to be sure my values are the same as the default values listed below. Thanks! Marc DICOM field (0019,1018) in s or "NONE" if not used T1wSampleSpacing="0.0000074" # DICOM field (0019,1018) in s or "NONE" if not used T2wSampleSpacing="0.0000021" On 19 Jul 2018, at 22:55, Harms, Michael wrote: As defined in the text comment, “ReconMatrixPE” is just the size (dimension) of your images in the PE direction. You don’t need to attempt to “derive” it from fields in the DICOM – just check your converted NIFTI itself! Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: Marc Dubin <[email protected]<mailto:[email protected]>> Date: Thursday, July 19, 2018 at 9:46 PM To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Cc: "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input I used the Matlab DICOM viewer and got BWPPPE as a private field, but did not see a field for ReconMatrixPE (is the latter a field in the DICOM header or computed from fields?) Thanks again! On 19 Jul 2018, at 22:36, Glasser, Matthew wrote: I would just pull the numbers directly from the indicated DICOM fields using a DICOM header viewer such as this one: https://wiki.xnat.org/xnat-tools/dicombrowser<https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.xnat.org_xnat-2Dtools_dicombrowser&d=DwMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=GqesNQY9bpJn68E36-I5WBDQNXo9kEZLUS292SO3PoE&s=7rBFGJ2tD4GOT8JdpYtKkt7yMEQXReaOMxgQNWKQIQs&e=> And then compute using the indicated formulas. Unfortunately it seems one of the field names has been deleted and now it is confusing, but here is what it used to say: https://github.com/Washington-University/HCPpipelines/commit/ca8c80ac7a615f8b8ebbd889b5f396bdcd788db8#diff-1bec2a8a1f62ce72a23680add2b08468<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_commit_ca8c80ac7a615f8b8ebbd889b5f396bdcd788db8-23diff-2D1bec2a8a1f62ce72a23680add2b08468&d=DwMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=GqesNQY9bpJn68E36-I5WBDQNXo9kEZLUS292SO3PoE&s=Z7LvjnrPy7s1J_JJiIMB0ztIa8zp_99rxBH-bXfEb8k&e=> Matt. From: Marc Dubin <[email protected]<mailto:[email protected]>> Date: Thursday, July 19, 2018 at 9:24 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input Thank you, Matthew! Is the Size of the reconstructed image in the PE (phase encoding) direction the same as the number of phase encoding steps (109 in the case of my scans)? Marc On 18 Jul 2018, at 9:11, Glasser, Matthew wrote: You need to follow the instructions listed to find those DICOM fields and put in the values. b02b0.cnf is fine. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Marc Dubin <[email protected]<mailto:[email protected]>> Date: Tuesday, July 17, 2018 at 11:29 PM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input Thank you, Michael! Do you know for this section: "Effective" Echo Spacing of Spin Echo Field Maps. Specified in seconds. # Set to "NONE" if not used. # SEEchoSpacing = 1/(BWPPPE * ReconMatrixPE) # where BWPPPE is the "BandwidthPerPixelPhaseEncode" = DICOM field (0019,1028) for Siemens, and # ReconMatrixPE = size of the reconstructed SEFM images in the PE dimension # In-plane acceleration, phase oversampling, phase resolution, phase field-of-view, and interpolation # all potentially need to be accounted for (which they are in Siemen's reported BWPPPE) # # Example value for when using Spin Echo Field Maps from the HCP-YA # 0.000580002668012 SEEchoSpacing="NONE" How I would know what the appropriate value of SEEchoSpacing would be for my data? Also, is it safe to assume: TopUpConfig="${HCPPIPEDIR_Config}/b02b0.cnf”. ? Thanks again! On 18 Jul 2018, at 0:20, Harms, Michael wrote: Hi, If you are using SEFMs, you don't need to generate magnitude and phase field maps. It is handled internally. See the Batch script in the Examples directory. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> On 7/17/18, 11:12 PM, "[email protected]<mailto:[email protected]> on behalf of Marc Dubin" <[email protected]<mailto:[email protected]> on behalf of [email protected]<mailto:[email protected]>> wrote: Dear All, I am new to the HCP MR pipelines and was wondering if anyone can provide guidance on how to generate magnitude and phase field maps for input to PreFreeSurferPipelineBatch.sh The files that I currently have from the Siemens 3T scanner are: SpinEchoFieldMap_PA SpinEchoFieldMap_AP Thanks for any suggestions!! Marc Dubin Marc Dubin, MD PhD Assistant Professor of Psychiatry and Neuroscience Department of Psychiatry and Brain and Mind Research Institute Weill Cornell Medicine | New York-Presbyterian Psychiatry-Box 140 525 East 68th Street New York, NY 10065 T 212.746.5817 [email protected]<mailto:[email protected]> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=FAIO2nXXbHnlQIPmBor8N3OKZ3Og-QBPPythGBiuwKA&s=j-Z3UnFpmcfrTtH1NnTvqxuJkBHYdMb0ZZvhZjB0iXc&e= ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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