Hi Mike, the intent was to be independent of the prescription of the slices so that we could always depend on voxel coordinates having some anatomical meaning, regardless of what crazy slice orientation was prescribed. Not sure if Doug has some easier work around for you to prevent the rotation.
cheers Bruce On Thu, 16 Jun 2011, Michael Harms wrote: > > Hi guys, > > I'm curious why the conform step of mri_convert (in generating > mri/orig.mgz) automatically interpolates oblique acquisitions. Is this > a historical legacy? Something mandated by other elements of the FS > pipeline? As a consequence of this behavior, if you have an oblique > acquisition that was intentionally aligned to the actual anatomy of a > given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned > acquisition), unless one manually alters the qform in the input NIFTI > file to remove the "oblique" components of the xform, there will be an > interpolation in the generation of the mri/orig.mgz, which brings with > it blurring (i.e., the same sort of concerns that prompt one to use a > single MPRAGE, rather than the average of two MPRAGEs) > > Just curious... > > thanks, > -MH > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
