FWIW, the readout distortion effect in the structurals is such a small effect that it is difficult to confirm the appropriate polarities for that correction by trial and error.
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 Keith Jamison <kjami...@umn.edu> Date: Thursday, August 30, 2018 at 8:51 AM To: "Glasser, Matthew" <glass...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, "Stevens, Michael" <michael.stev...@hhchealth.org> Subject: Re: [HCP-Users] TOPUP Settings Note: The --UnwarpDir in PreFreeSurfer is the readout direction of the T1w and T2w images themselves, which in this case is completely unrelated to the plane in which the SE fieldmaps read out (which is set in --SEUnwarpDir). fMRI and DWI are 2D and their unwarpdir are more obvious. For the 3D T1w and T2w sequences, the readout direction in which most distortion occurs is trickier to figure out, which is why Matt suggests trial and error. For HCP acquisitions it's always been "z". -Keith On Wed, Aug 29, 2018 at 7:02 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Hi Mike, As far as I know the only sure way is with trial and error, but perhaps the latest dcm2niix has eliminated that. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Stevens, Michael" <michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>> Date: Wednesday, August 29, 2018 at 5:54 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] TOPUP Settings Also, I’d like to confirm some settings for the HCP scripts, as I’m helping some colleagues set up a new protocol that we plan to use HCP pipeline processing on. For spin echo-based unwarping, if HCP’s standard SE field map sequences are used and are acquired A>>P first, P>>A second, should the proper setting for UnwarpDir in the PreFreeSurfer script unwarping of the T1w image be ‘y’ or ‘y-‘? And further… Shouldn’t the same UnwarpDir setting be used for fMRI unwarping? I set my own HCP protocols up a couple of years back and I’m straining my memory to recall exactly how the HCP scripts parse all this and create the commands that call topup. I’m hoping to avoid some painstaking trial-and-error by asking. Thanks, Mike 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<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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
