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 Iopened 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, MarkThe 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.
