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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer