> > I would focus your attention on the initial rigid alignment done in > epi_reg (before BBR and the distortion correction). This step we have > found is sometimes not robust, particularly when acquisition protocols > deviate from the recommended ones. It isn’t BBR based and doesn’t yet have > the data in rough alignment (generally pipeline failures occur at initial > stages, if the initial stages work, generally everything else is more > robust). > yes, this is where the problem occurs; more specifically, in the magnitude fieldmap to structural registration with flirt, line 346 of epi_reg (I realize now that "Scout_gdc_undistorted_" is the prefix for all files output by epi_reg [because Scout_gdc_undistorted.nii.gz is the final output of the epi_reg script], which is the info that I was missing to debug the alignment). I'm all set now. Thanks for your help.
> > I understand you are working with legacy data, it’s just important to > note that the amount of work required to make legacy data work with the HCP > Pipelines is not indicative of the amount of work required when following > the image acquisition guidelines. We’re still willing to provide > suggestions as to what to look at when getting the legacy data to work, but > cannot fully support legacy data (e.g. you have to hack some on your own > and figure it out). Also, not all pipeline changes required when working > with legacy data may be generally applicable to all data (so we’ll consider > this when considering patches that come from trying to get legacy data to > work). > Point taken, I will refrain from posting to this list about legacy data - unless I think it is a more generic issue. - Julien _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
