That note in the pipeline example code was put there because I don¹t know how to tell what readout direction was used from the DICOMs and z seems to be the Siemens default. If someone else does, I¹d be interested in what field(s) they used.
Gordon, I¹d be a bit surprised here if the shim mattered given how small the correction is already and the fact that the bulk of the correction is likely to be the same from one shim to another. I don¹t think it¹s likely to be made worse by reshiming, just won¹t be quite as precise of a correction. Peace, Matt. On 10/24/14, 10:33 PM, "Xu, Junqian" <[email protected]> wrote: >As for importance, it depends on your application but readout distortion >is typically quite small. Btw, we¹ve observed that the scanner >re-shimming often happens between the fieldmap and the structural scans >if the scanner operator is not well-educated for the importance of >preventing re-shimming. In such cases, I think it is better to disable >the readout distortion correction in the PreFreeSurferPipeline. > >Gordon > >> On Oct 24, 2014, at 11:18 PM, Xu, Junqian <[email protected]> wrote: >> >> 'Unwarp Dir¹ should correspond to the Readout (frequency encoding) >>direction for the ŒPreFreeSurferPipeline', in which case is the Z >>direction (Head - Foot) for the sagittal T1w/T2w HCP structural >>acquisitions. Not sure what you mean by "The only comment is that z >>appears best.² Below is what¹s in PreFreeSurfer/PreFreeSurferPipeline.sh >> >> --unwarpdir={x, y, z} Readout direction of the T1w and T2w >>images >> (Used with either a regular >>field map or a spin >> echo field map) >> >> >>> On Oct 24, 2014, at 8:28 PM, Micah Chambers <[email protected]> >>>wrote: >>> >>> Could anyone provide a better explanation of the importance of Unwarp >>>Dir in the example file 'PreFreeSurferPipelineBatch.sh'? The only >>>comment is that z appears best. It seems like direction of warping >>>should be a known value, is that not the case. >>> >>> I don't know if this is related, but I have been testing the scripts >>>with HCP subject 901038 and I am finding that the outputs do not match >>>up. There is a slight tilt to the head. While not a big issue (the >>>brain is still labeled correctly), it makes validation of scripts >>>harder. Has anyone else had such an issue? I have included screenshots >>>(ours.png is our local version, hcp.png is the downloaded version). >>>Note that this came from '901038_3T_Structural_preproc.zip' and was >>>downloaded about a month ago. >>> >>> Thanks >>> >>> -MIcah >>> >>> -- >>> Micah Chambers, M.S. >>> Ahmanson-Lovelace Brain Mapping Center >>> University of California Los Angeles >>> 635 Charles E. Young Drive SW, Suite 225 >>> Los Angeles, CA 90095-7334 >>> 310-206-2101 (Office) >>> 310-206-5518 (Fax) >>> 703-307-7692 (Cell) >>> email: [email protected] >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> >>>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectom >>>e.org_mailman_listinfo_hcp-2Dusers&d=AAIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8 >>>m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=UEyeqf >>>3jP4WJpWQN5X0VinWErEJz5X0LwGv9I9bKTaE&s=VGju-usV7cI7ZgqageB_YKPSrZ9SFw22 >>>f0BHVq4UfxA&e= >>> >>> <ours.png><hcp.png> >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> >>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome >>.org_mailman_listinfo_hcp-2Dusers&d=AAIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8 >>VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=UEyeqf3jP >>4WJpWQN5X0VinWErEJz5X0LwGv9I9bKTaE&s=VGju-usV7cI7ZgqageB_YKPSrZ9SFw22f0BH >>Vq4UfxA&e= > > >_______________________________________________ >HCP-Users mailing list >[email protected] >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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
