Garth,
I spoke too soon. Looking at the files in your mri/orig directory,
001.mgz is a structural, but 002.mgz appears to be an epi (partial
brain), so the orig.mgz is a mix of the two (with the wacky intensity
profile).
You should delete 002.mgz and either just run with 001.mgz (which looks
goo
sure. Good luck.
Bruce
On Tue, 18 Aug 2009, Garth Coombs wrote:
> 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
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
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 wa
Hi Garth,
sorry, I don't understand. You can try running mri_normalize without the
tal stuff by giving it -no1d (you can find the full command line in the
scripts/recon-all.log file). If the tal is too far off it will cause the
first step (the 1d part) of the normalization to fail.
cheers,
Bru
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 possib
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
>
