Perhaps Mike and Tim could help. Matt.
From: Osama Abdullah <o...@nyu.edu<mailto:o...@nyu.edu>> Date: Thursday, January 11, 2018 at 10:48 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "at...@nyu.edu<mailto:at...@nyu.edu>" <at...@nyu.edu<mailto:at...@nyu.edu>> Subject: Re: [HCP-Users] volumetric BOLD time series in Native Space? Thanks Matt. Yes, would it be possible to get the warpfields (gradient nonlinearity, motion correction, distortion correction, and fMRI to T1 native) so that we can combine in single step resampling? Not sure what’s the REST interface. But I am happy to compare the two options. All the best. Osama On Jan 11, 2018, at 5:42 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I don’t know that we provide the files to do this yourself in the packages. We could consider providing the gradient nonlinearity warpfield, the motion correction matrices, the distortion correction warpfield, and the fMRI to T1w transformation matrix. Alternatively, you could resample the MNI space timeseries with splines back to T1w space. This will induce some slight smoothing relative to having done this natively, but I am guessing it will not be that different (particularly because of the drift in MNI space which leads to an expansion). If you are interested in comparing the two options, we could probably help you get the intermediate files using the REST interface. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Thursday, January 11, 2018 at 12:29 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "at...@nyu.edu<mailto:at...@nyu.edu>" <at...@nyu.edu<mailto:at...@nyu.edu>>, "o...@nyu.edu<mailto:o...@nyu.edu>" <o...@nyu.edu<mailto:o...@nyu.edu>> Subject: [HCP-Users] volumetric BOLD time series in Native Space? Dear HCP'ers, When using the Minimal Preprocessing Pipeline, seems we don't get native-space-registered-to-nativeT1 BOLD time series that is gradient-distortion-corrected, motion-corrected, and EPI distortion corrected? Am I missing it or does not exist? If it doesn't exist, what would be the required modification to the "One Step Spline Resampling" step to apply all the corrections except the MNI-registraion step? Many thanks for your continued superb work. Regards. Osama _______________________________________________ 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
