Ahh, I found the problem. The talairach.lta is completely off. You can tell in the attached image. It also seems that the slice #'s are not lining up correctly. For instance, the 128th slice (of the talairach) in the horizontal view looks like it should correspond to maybe slice 50 (it is nearly non-existant). Any ideas on how to fix these problems? 


On Fri, Jan 17, 2014 at 4:16 PM, Mark Plantz <markplantz2016@u.northwestern.edu> wrote:
I actually just tried to test the talairach.lta with this command:

tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \
  --targ ../brainmask.mgz --lta-inv talairach.lta --reg 
talairach.lta.reg.dat \
  --surfs --s $subject
I seem to be getting an error that "--lta-inv is not an option". Is there another way to check talairach.lta?


On Fri, Jan 17, 2014 at 4:06 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
see if the talairach.lta looks reasonable


On Fri, 17 Jan 2014, Mark Plantz wrote:

Hi Bruce,
    The nu.mgz file looks OK to me (I also attached a picture). When I
opened the talairach with "tkregister2" everything looked ok, except I
couldn't get the green lines from the original surface to show (even after
pressing 's' in the viewing window). Anyways, since these two files seem to
be OK, do you think it is an atlas issue?

Thank you!

- MP


On Thu, Jan 16, 2014 at 7:36 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Mark

      does the input to mri_ca_normalize look ok (the nu.mgz)? Is the
      talairach.xfm ok?

      Bruce
      On Thu, 16 Jan 2014, Mark Plantz wrote:

            Hello freesurfers,

                 I am running into a problem during the "CA
            Normalize" sequence of
            autorecon-2. It looks like freesurfer is having a
            hard time creating control
            points based off the atlas I am using. The output is
            as follows:

            "finding control points in
            <Left_Cerebral_White_Matter>...found  0 control
            points"

                  This repeated for the other various regions
            included in the atlas. The
            only control points found were "168 control points"
            in the
            "Right_Cerebral_White_Matter". Could this possibly
            be an alignment issue? If
            so, is there an easy way to check the alignment?

            Thank you,


            Mark








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