If you pull the most recent (master) version of PreFreeSurferPipelineBatch.sh from GitHub, you'll get one in which we recently improved the comments to hopefully make things clearer.
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 On 7/17/18, 11:48 PM, "Marc Dubin" <mrd9...@med.cornell.edu> wrote: Hi Michael, Another quick question… What would be appropriate values for: DwellTime SEUnwarpDir TopupConfig Thanks! Marc 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 > On 7/17/18, 11:12 PM, "hcp-users-boun...@humanconnectome.org on > behalf of Marc Dubin" <hcp-users-boun...@humanconnectome.org on behalf > of 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 > _______________________________________________ > HCP-Users mailing list > 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. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
