Hi Doug, Do you have any comment regarding the easiest way to prevent interpolation of oblique acquisitions at the conform step of the FS pipeline?
thanks, -MH On Thu, 2011-06-16 at 21:21 -0400, Bruce Fischl wrote: > 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 > > > > > > > > > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
