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.eduwrote:

...

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

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.