And to answer your original question, NO, the number of phase encoding steps is not necessarily the same as the size of the *reconstructed* image.
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: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael" <mha...@wustl.edu> Date: Thursday, July 19, 2018 at 9:44 PM To: "Glasser, Matthew" <glass...@wustl.edu>, Marc Dubin <mrd9...@med.cornell.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input Use the text in the current master as your guide (not the older guidance) because the current guidance has been specifically constructed to be accurate in all known situations with Siemens data, include partial fourier, in-plane acceleration, phase oversampling, interpolation, etc, etc. If you are using a modern version of ‘dcm2niix’ for your DICOM to NIFTI conversion, the necessary values are all provided for you as part of the BIDS sidecar (.json) file. 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: mha...@wustl.edu From: "Glasser, Matthew" <glass...@wustl.edu> Date: Thursday, July 19, 2018 at 9:36 PM To: Marc Dubin <mrd9...@med.cornell.edu> Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input 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 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 Matt. From: Marc Dubin <mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu>> Date: Thursday, July 19, 2018 at 9:24 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marc Dubin <mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu>> Date: Tuesday, July 17, 2018 at 11:29 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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: mha...@wustl.edu<mailto:mha...@wustl.edu> On 7/17/18, 11:12 PM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Marc Dubin" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu>> 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 mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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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