Re: [HCP-Users] spin echo phase encoding direction

[Harms, Michael]

The value of "PhaseEncodingDirectionPositive" in the shadow field (0029,1020) reflects the combination of both "Phase enc. dir." on the Routine tab (e.g., "A>>P" vs. "P>>A") AND the setting of "Invert RO/PE Polarity" on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction.   I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results.  That's because the correct setting for PhaseEncodeList (e.g., "y-" vs. "y+") can in theory even be dependent on which DICOM to NIFTI converter you use.  (e.g., if one converter returns a +LAS orientation, while another returns a +LPS orientation, then the proper settings for PhaseEncodeList may be swapped). 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: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Monday, December 15, 2014 8:38 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question!   It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We’ve been collecting the EPI images without this inversion. So, for our data: EPI is A>>P “A>>P” SE is actually P>>A “P>>A” SE is actually A>>P   Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=”task1” PhaseEncodeList=”y-“ … SpinEchoPositiveImage=”the P>>A labeled image (actually acquired A>>P)” SpinEchoNegativeImage=”the A>>P labeled image (actually acquired P>>A)”   -G   _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net   This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ 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