I usually get confused myself when dealing with compositions of warps, and
have to refer to the example in Section 1.4 of the Dartel Guide. I find this
sort of thing is much easier to figure out with by equations than with words.
When creating a warped an image, the usual approach is to scan through the
image to be created. For each voxel (of the new image, which is to be
created), the resampling needs to figure out where in the original image to
read the value from. In other words, it needs a mapping from coordinates in
the new image, to coordinates in the original.
>If I
> Normalise: Estimate with Image1 as the source and Image2 as the template,
> then the resulting *sn.mat transforms from Image1 (source) to Image2
> (template), and this is called the "map" or "mapping" from Image2
> (template) to Image1 (source)?
Yes. The algorithm needs to know where in image 1 to read the values from.
> Also, a forward DARTEL flow u_* transforms
> from template to individual, and this is a "mapping" from individual to
> template?
The DARTEL u_* can be used to transform either way. In the Deformations
utility, I used "backward" to mean something that will warp an individual
scan to the template.
> And if this is correct, does "Create Warped" apply the backward
> transform?
Yes.
> Based on the example in the manual, I believe the way I am supposed to
> enter the warps/maps to get a deformation from Time1 to MNI space is:
>
> 1) Flow field from within-subject DARTEL (warp of Time1 to individual
> template, a.k.a. mapping of individual template to Time1) - backward
>
> 2) Flow field from between-subject DARTEL (warp of individual template
> to group template, a.k.a. mapping of group template to individual template)
> - backward
>
> 3) *sn.mat from Normalise:Estimate of group template to MNI template
> (mapping from MNI space to group template)
>
> Would someone please let me know if this is correct?
That looks entirely correct.
Note that the transform does not work with "imported" images (clue: try a
Check Reg with an imported image and an original), but it should work on the
originals and any images in alignment with them (according to Check Reg).
All the best,
-John
On Monday 15 December 2008 21:15, Dana Perantie wrote:
> Dear SPM and DARTEL experts,
> I am doing longitudinal DARTEL and I am at the step of combining multiple
> warps (e.g., Time1 to individual template, individual template to group
> template, and group template to MNI). I want to make sure I am combining
> them in the proper order and direction. I want to clarify the term
> "mapping" as it used in the manual. Do I understand correctly: If I
> Normalise: Estimate with Image1 as the source and Image2 as the template,
> then the resulting *sn.mat transforms from Image1 (source) to Image2
> (template), and this is called the "map" or "mapping" from Image2
> (template) to Image1 (source)? Also, a forward DARTEL flow u_* transforms
> from template to individual, and this is a "mapping" from individual to
> template? And if this is correct, does "Create Warped" apply the backward
> transform?
>
> Based on the example in the manual, I believe the way I am supposed to
> enter the warps/maps to get a deformation from Time1 to MNI space is:
>
> 1) Flow field from within-subject DARTEL (warp of Time1 to individual
> template, a.k.a. mapping of individual template to Time1) - backward
>
> 2) Flow field from between-subject DARTEL (warp of individual template
> to group template, a.k.a. mapping of group template to individual template)
> - backward
>
> 3) *sn.mat from Normalise:Estimate of group template to MNI template
> (mapping from MNI space to group template)
>
> Would someone please let me know if this is correct?
> Thank you,
> Dana
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