Dear John,
My MATLAB coding knowledge is limited, but I looked at the functions you mentioned and I sort of understand. I am able to produce the composition (A o B) as a y_warp.nii. Is there a way to translate j and/or y (from dartel3 function) into an *sn.mat file, or modulate an image by j or y? How do y and j relate to the matrices Affine and Tr? Tr for our images have the dimensions 6 x 9 x 10 x 3 -- is that always the case, and can you tell me what each of these dimensions refers to? When you used dartel3 below, how did you pick 6 as the number of recursions?
Thanks again,
Dana
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: Wednesday, October 29, 2008 9:35 AM
To: Dana Perantie; [log in to unmask]
Subject: Re: [SPM] combining non-linear warps
Dear Dana,
There's nothing in the Deformations Utility for doing this in a nice easy way,
but it could be done by working with the Jacobian fields that can be written
out to disk. The toolbox/DARTEL/spm_dartel_norm.m function is used for
writing normalised data.
I'm not sure how your MATLAB coding is, but you could do it using some code
along the lines of...
N1 = nifti('u_image1.nii');
N2 = nifti('u_image1.nii');
u1 = squeeze(single(N1.dat(:,:,:,:,:)));
u2 = squeeze(single(N2.dat(:,:,:,:,:)));
[y1,j1] = dartel3('Exp', u1, [6 1 1]);
[y2,j2] = dartel3('Exp', u2, [6 -1 1]);
y3 = dartel3('comp', y1, y2);
j3 = dartel3('samp',j1,y2).*j2;
There'll be a bit more to it than this though.
All the best,
-John
On Tuesday 28 October 2008 19:34, Dana Perantie wrote:
> Thanks John,
> The Deformations utility is going to be very helpful, and so are the
> instructions in the DARTEL manual.
>
> Is there also a simple way to "modulate" by a flow field *without* applying
> the flow field at the same time? I want to warp a whole brain image by A
> and later by B, segment the output of that and then modulate the segments
> by the composition (A o B). If there is not already a GUI to do that, could
> you please point me to the *.m file for DARTEL's "Create Warped" so I may
> pick out the modulation step from there?
>
> Thanks again,
> Dana
>
>
> -----Original Message-----
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: Friday, October 17, 2008 10:16 AM
> To: Dana Perantie; [log in to unmask]
> Subject: Re: [SPM] combining non-linear warps
>
> I forgot to mention that the approach involves the Deformations utility,
> available from the Tasks pulldown. There is some documentation about how
> to use it in the http://www.fil.ion.ucl.ac.uk/~john/misc/dartel_guide.pdf
> file (or the SPM8b manual).
>
> Best regards,
> -John
>
> -----Original Message-----
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: Friday, October 17, 2008 10:14 AM
> To: Dana Perantie; [log in to unmask]
> Subject: Re: [SPM] combining non-linear warps
>
> There's no tool for generating a new sn.mat file, but you can generate a
> y_*.nii, which could be used for the same thing.
>
> Best regards,
> -John
>
> On Thursday 16 October 2008 21:07, Dana Perantie wrote:
> > Hello SPM list,
> > Is there a way to combine non-linear warp parameters, i.e. if I warp A to
> > B and B to C, is there a way to combine the *sn.mat files to make a *.mat
> > representing the warp from A to C? Thank you,
> > Dana
