Here is the full message when I tried it with control pts.:

freesurfer/subjects> mri_normalize -f TFL_2107_6/tmp/control.dat TFL_2107_6/mri/orig/ TFL_2107_6/mri/T1/ using control points from file TFL_2107_6/tmp/control.dat... reading from TFL_2107_6/mri/orig/... normalizing image... talairach transform 1.082 -0.011 0.080 -3.369; 0.014 1.029 -0.038 -57.509; -0.085 0.044 1.157 -35.175; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory

Quoting Evelina Busa evelina@nmr.mgh.harvard.edu:

YOU> Hi Keyma! YOU> YOU> Could you send the command you used, and possibly more output? (say, the YOU> YOU> last 15 lines before the error message?) YOU> YOU> Thanks! YOU> YOU> On Mon, 26 Jul 2004, Chekema 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> YOU>

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>

Dear list,

This issue was probably already discussed (couldn't find it), but I wanted to make sure that I'm correct before proceeding. In order to extract a patch of surface from the average brain, can I just draw a label on whatever surface configuration I display it on? Also, how to load the probabilistic values obtained as a result into Matlab?

thanks in advance,

-Oleg