Re: [HCP-Users] Field Map

[Harms, Michael]

Hi Peka, I'm not quite sure what you have, but an axial FLAIR scan with CLEAR applied seems like it would be a structural scan, not a field map. Even if you have a dual-echo gradient echo field map acquisition, I'm afraid that the pipelines haven't been extended yet to incorporate whatever is the "standard" Philips field map output format.  Depending on whether Philips outputs a "Phase" volume, and if so, the nature of this volume, you might be able to treat your inputs similar to the use of Siemens acquired gradient echo field maps, but I suspect that at least some pipeline modifications would be necessary on your part. Your best bet is to probably start with the FUGUE guide on the FSL website http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE coupled with studying the pipeline code for how the Siemens field maps are handled. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders 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: Peka Savayan <savay...@umn.edu> Date: Tuesday, January 5, 2016 10:31 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Field Map Dear Experts, I need your advice using Field Map (FM). I have an FM from a Philips Achieva 3T 32channel coil. I believe it is from an in-scanner image intensity equalizing algorithm (i.e., Constant Level AppeaRance, CLEAR) with series description FLAIR_Ax CLEAR. How can I use this file in the pipeline?  Specifically: Can you please give me detailed step by step procedures on how to generate the Magnitude and Phase? I appreciate your time and efforts. Sincerely, Peka _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   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