If you have spm, you can use --init-spm. Alternatively, you can use mri_coreg instead of bbr (bbr is not as effective on blurry data)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta
Also, why is the top of the head cut off? That makes it much more difficult to register.
doug
On 2/22/16 8:02 PM, Pradeep wrote:
Hello All,
I am trying to map pet scans to MRI using bbregister and quite a few subjects were improperly registered.
Here are my steps: bbregister --s $fs --mov ${pet_ext}_LIA.nii --init-fsl --t1 --lta output.lta tkregister2 --mov summed_LIA.nii --reg output.dat --surf
[ mri]$ more output.dat.mincost 0.860663 0.000513 0.000492 -11.863233 The first value is quite close to 1 so its bad
I have attached a screen shot of the image and the log file generated after bbregister. Please let me know if there are any parameters that I could tweak to make the registration better.
Thank you for your help, -Pradeep
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