Yousef wrote:

> Dear AFNI:
>
> I am working on a problem to allign
> step 1: a warped MR image (source) to another MR image (target)
> obtained at a different date.
> step 2: Allign a MR volume with CT images.
>
> Question 1 : Can AFNI perform such an analysis?
Yep

>
> Question 2: 3dAllineate - Is 3dAllineate appropriate for
> alligning MR with non-MR images (such as CT, PET, etc.)?
Correct

>
> Question 3: 3dAllineate- 1Dparam_apply are 1-D warp parameters.
> How could this perform spatial transformation that accounts for
> non-rigid transformation of images.
3dAllineate only goes up to 12 parameters (shift, rotation, stretch, shear)
>
> Question 4: 3dAllineate - uses header information. GIven that
> the two MR data were acquired on separate days, the header
> information is not useful.
I don't see why that would be the case. I don't think you need to worry about that. If the datasets are way out of alignment, you can first use @Align_Centers to bring the volumes into a coarse alignment.
>
> I would greatly appreicate your help
>
> Thank you very much
>
> Yousef


cheers,
AFNI