Thanks a lot,
I'll use your solution, I think it's the fastest solution for now.
I'm still not sure however why a more straightforward solution is
flawed. From what I saw in SPM's manual, the normalization step first
computes (before actually warping the two volumes) what every
alignment algorithm computes - a transformation from the source
coordinates to the target coordinates. (But maybe I missed a few
details about the implementation).
On Sun, Jun 5, 2011 at 10:49 AM, Michael T Rubens <[log in to unmask]> wrote:
> only if you disregard the process of normalization. Its not as simple as
> voxel x in source image corresponds to voxel y in template image. The
> normalization depends on several factors, including intensity and smoothing
> parameters, so even if you could find code that attempts to do that it would
> be flawed. I would just code it up the way I said to do it, but good luck
> looking for the code that makes sense to you.
>
> Cheers
> On Sun, Jun 5, 2011 at 12:38 AM, Yonatan Dinai <[log in to unmask]> wrote:
>>
>> Thanks Michael.
>> I think it would make sense to have a more straightforward function
>> that does a transformation for any set of input points.
>>
>>
>>
>> On Sun, Jun 5, 2011 at 8:08 AM, Michael T Rubens <[log in to unmask]>
>> wrote:
>> > Just estimate the transformation without writing, then write without
>> > estimating using the calculated transform to warp an image with the
>> > coordinates you want normalized set to 1, and all others 0. Then just
>> > look
>> > for all non-zero voxels after the transformation.
>> >
>> > Cheers,
>> > Michael
>> >
>> > On Sat, Jun 4, 2011 at 9:49 PM, Yonatan Dinai <[log in to unmask]>
>> > wrote:
>> >>
>> >> Hello all,
>> >>
>> >> I've used the "normalize" function of SPM, and was able to warp two
>> >> volumes succesfully.
>> >>
>> >> I would now like to use the output parameters of the normalization
>> >> process - the 4x4 matrix of the affine transformation & the 4D matrix
>> >> of the DCT coefficients to transform an input point (X,Y,Z in the
>> >> source volume) into it's mapped point in the reference coordinates?
>> >>
>> >> Does anybody has a code the computes that transformation? Is there
>> >> such a function on SPM? If not, I would be happy to hear of any fast
>> >> way to compute such a transformation.
>> >>
>> >> Thanks a lot,
>> >>
>> >> Yonatan
>> >
>> >
>> >
>> > --
>> > Research Associate
>> > Gazzaley Lab
>> > Department of Neurology
>> > University of California, San Francisco
>> >
>
>
>
> --
> Research Associate
> Gazzaley Lab
> Department of Neurology
> University of California, San Francisco
>
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