Actually, bbregister has to be used to register the conformed anatomical to the diffusion. You can get the rawavg-to-dti registration with several steps.
1. bbregsiter with the diffusion lowb. Call this reg1.dat 2. Get the rawavg to conformed registration with: tkregister2 --mov rawavg.mgz --targ orig.mgz --regheader --reg reg2.dat --noedit 3. Get the final registration (reg3.dat) with mri_matrix_multiply -im reg1.dat -iim reg2.dat -om reg3.dat
4. Make sure this registration works: tkregister2 --mov lowb.nii --targ rawavg.mgz --reg reg3.dat 5. Convert the raw avg to the diffusion space: mri_vol2vol --mov lowb.nii --targ rawavg.mgz --reg reg3.dat --inv --o rawavg-in-diffusion.nii
doug
Bruce Fischl wrote:
Hi Jared
use bbregister as usual then you can use mri_convert with -ait to apply the inverse transform.
cheers Bruce On Tue, 12 Oct 2010, Tanner,Jared J wrote:
Hi,
Is there a way to use bbregister to register a FreeSurfer image (e.g., rawavg.mgz) to a diffusion image from the same participant? In other words, is there a way to specify --mov rawavg.mgz and make the target (template) image a b0 diffusion image? Or at least to perform an inverse transform on the rawavg image after registering the b0 to the rawavg?
I plan on trying mris_cvs_register but I was wondering if bbregister can do what I want.
I've used flirt, fnirt, and SyN registration methods but flirt isn't quite accurate enough for intra-subject, multi-modal registration, fnirt is better but still has troubles with cortical regions, and SyN has been too variable with results.
Thank you,
Jared Tanner PhD Candidate Clinical & Health Psychology University of Florida _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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