Hi, Note that UnwarpDir in the PreFreeSurfer script is a very different thing from UnwarpDir in the fMRIVolume script. In the former, it specifies the *readout* direction of the *structurals* -- typically ‘z’ for how we collect T1 and T2 structurals on Siemens scanners (assuming that the NIFTI you are using as input is either “LAS” or “RAS” oriented!!). In the latter, it is the *phase encoding* direction of the *BOLD* scan.
In the PreFreeSurfer script, the phase encoding direction of the ancillary SE field map scans is specified by the SEUnwarpDir variable. If those are AP/PA, we use SEUnwarpDir = y, and enter the SpinEchoFieldMap_PA scan as the input for the SpinEchoPhaseEncodePositive variable, and the SpinEchoFieldMap_AP scan as the input for the SpinEchoPhaseEncodeNegative variable. 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 "Glasser, Matthew" <glass...@wustl.edu> Date: Wednesday, August 29, 2018 at 6:03 PM To: "Stevens, Michael" <michael.stev...@hhchealth.org>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] TOPUP Settings 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 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
