Hi Nick and Bruce, I followed those instructions and am rerunning the recon, so hopefully that will solve the problem. I'll let you know if any other issues arise with this patient. Thanks for your help!
-Garth On Aug 18, 2009, at 11:03 AM, Nick Schmansky wrote: > Garth, > > I had a look at the subject in tkregister, and it is badly misaligned, > in a way that explains the intensity normalization problem. Follow > these > instructions to correct it: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Also, I'll take a look at why our tal alignment code was not able to > handle this image. > > Nick > > > > On Tue, 2009-08-18 at 10:05 -0400, Garth Coombs wrote: >> When I check the talairach.xfm using tkregister2 --mgz --s >> amcg_anat -- >> fstal --surf orig, it does not extend into the "darker" portion of >> the >> cortex and cuts short as if the cortex has been shaved off, but is >> only slightly off. In other areas, it looks very misaligned. It looks >> like possibly since it's not recognizing the cortex as brain, it's >> attempting to shift the whole alignment and aligning medial slices >> with more lateral slices so that the overall "height" of the cortex >> it's recognizing matches. I hope that makes sense. I would take a >> couple of pictures of it, but I'm not sure how to do so in >> tkregister2. >> >> >> >> On Aug 17, 2009, at 5:40 PM, Bruce Fischl wrote: >> >>> wow, I haven't seen that before. Can you check the talairach.xfm >>> and see if it's correct? >>> On Mon, 17 Aug 2009, Garth Coombs wrote: >>> >>>> Hi, >>>> >>>> I am running a patient of ours with some cortical degeneration >>>> through the recon process and have run across an interesting >>>> problem. It appears as if the intensity normalization process is >>>> missing a large portion of the cortex, resulting in an almost >>>> straight line through the middle of his head, with the center >>>> portion looking like the intensity normalization worked, but the >>>> cortex portion is very dark. The white matter in the cortex hasn't >>>> been normalized, and some of the gray matter looks as if it has >>>> been washed out or stripped away (that may just be due to the >>>> degeneration though). I have been going through and attempting to >>>> pick out control points to run -autorecon2-cp, but we wanted to >>>> check in and see if that was the best course of action for this >>>> particular subject before I got too far into it. >>>> >>>> The data can be found in /autofs/space/dinah_001/users/balaji/ >>>> SUBJECTS_DIR/subjects/ and the subject ID is amcg_anat >>>> >>>> Any advice would be greatly appreciated. >>>> >>>> Thanks! >>>> >>>> -Garth >>>> >>>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
