there is a 1d normalization that is the first step to approximately center the intensities at 110 in horizontal slices. This depends on talairach, and won't work if it failed, and isn't really necessary if you have manually picked some control points.
cheers, Bruce
On Tue, 27 Jul 2004, Chekema Nayasha Prince wrote:
Thanks the -no1d flag worked.
What does this flag change about the normalization process?
-Keyma
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
YOU> run it with -no1d. Also, check the talairach. YOU> YOU> Bruce YOU> YOU> On Mon, 26 Jul 2004, Chekema YOU> Nayasha Prince wrote: YOU> YOU> > Hello, YOU> > YOU> > I'm trying to normalize an MPRAGE dataset and I received the following YOU> message YOU> > from the mri_normalize: YOU> > YOU> > MRInormalize:could not find any valid peaks YOU> > no such file or directory YOU> > mri_normalize: normalization failed YOU> > no such file or directory YOU> > YOU> > I tried to set control points ( 4 of them specifically) in the wm and YOU> tried to YOU> > rerun the mri_normalize but I received the same error. YOU> > YOU> > my orig volume looks just like my other datasets that worked properly. YOU> Can you YOU> > let me know what could be causing the error? YOU> > YOU> > -Keyma YOU> > YOU> > YOU> > YOU> > _______________________________________________ YOU> > Freesurfer mailing list YOU> > Freesurfer@nmr.mgh.harvard.edu YOU> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer YOU> > YOU>