> Thank you, John.  I understand all but your last sentence.  The u* can be
> applied to the DARTEL-imported images (Create Warped is applied to
> rc1*.nii), but the transform that was made by combining u* flow fields
> cannot be applied to the imported images?  I would have guessed the other
> way around - that they could not be applied to the original-native-space
> images.  Are the u* files flow fields between the imported images and the
> resulting template, or original-native-space and the resulting template?

The deformation fields are generated so that there is a mapping to the images 
prior to their being imported, rather than to the imported images.  I figured 
that this would be generally more useful.  It is possible to achieve because 
the imported images (and u_*.nii files) contain two different matrices in 
their headers.  One of them (the one used by Display and Check Reg) shows the 
imported images in alignment with each other.  The other one (not used by 
Display and Check Reg) contains a mapping that relates the imported to the 
original image.

> We made a script (attached) to convert the y* deformation field to Jacobian
> determinant image that can be used to multiply/modulate.  This was based on
> snippets of HDW scripts as suggested in previous posts.  Our next step is
> to make a script to do it in a batch: calculate the compositions y*,
> translate to Jacobians and modulate (for a list of subjects at multiple
> timepoints).

That's a good approach.

Best regards,
-John

>
>
>
> -----Original Message-----
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: Wednesday, December 17, 2008 1:02 PM
> To: Dana Perantie; [log in to unmask]
> Subject: Re: [SPM] forward/backward flow, warp, map
>
> 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