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 <fis...@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 <fis...@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. >> >> >> >> >>
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