There are a couple of things in SPM8 that would achieve this.
1) Coreg: Reslice Only. Select the DARTEL-created template as the reference.
2) ImCalc. Select the DARTEL-created template and the AAL-based mask
and evaluate a function "i2".
Note that repeatedly resampling using NN interpolation will degrade
the images. Ideally, you'd compose the various deformations using the
Deformations utility, and warp the image this way. This is slightly
tricky to use though, and you may need to play around with it until
you understand what it really does.
Best regards,
-John
2012/1/31 Ko, Ji Hyun <[log in to unmask]>
>
> Hi,
>
>
>
> I have encountered similar problem, so I am posting a question under this thread.
>
>
>
> Now, I am warping the AAL-based mask into my template (DARTEL created avg T1).
>
> But it gives me an error message that the dimensions are incompatible.
>
>
>
> I checked that the AAL-based mask is 121x145x121x2 while the DARTEL-created template is 79x95x68x2.
>
>
>
> AAL-based mask was processed with "new segment".
>
>
>
> Is there any easy step to make the AAL-based mask to have reduced dimension?
>
>
>
> Best,
>
>
>
> Ji Hyun
>
>
>
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: Wednesday, January 04, 2012 12:12 PM
> To: [log in to unmask]
> Subject: Re: Question about transformation
>
>
>
> Sorry, but I misunderstood your original question. When you said transformation matrix, I assumed that you meant affine transformation matrix. The deformation fields for nonlinear registration are not really matrices (although you can conceptualise the combination of spatial transformation and interpolation as being the result of multiplying by a very large sparse matrix).
>
> The AAL atlas is just based on the brain of a single subject, which has been affine transformed to MNI space. Therefore, you'll need to find the deformation that warps this subject so he matches your Dartel template. To do this, you could try running the segmentation on a copy of the spm8/canonical/single_subj_T1.nii file to generate imported GM maps, and then running the "Run DARTEL (existing templates)" option to bring this into alignment with your Dartel template data.
>
> When you have used Dartel, you can warp the AAL atlas to match your subject as described in section 42.4 of the SPM8 manual (Warping one individual to match another). As you are warping an image of labels, you should change the interpolation to nearest neighbour.
>
> Best regards,
> -John
>
> 2012/1/4 YAN Chao-Gan <[log in to unmask]>
>
> Dear John,
>
> Then M ("M is the appropriate matrix") is very important to get. In Unified Segmentation, we can get it from *_seg_inv.mat . For the instance in New Segment + DARTEL, how can we get it?
>
> Thanks,
>
> Chao-Gan
>
>
>
> 2012/1/4 John Ashburner <[log in to unmask]>
>
> It's not so straightforward to do this sort of thing by clicking buttons via the user interface, but if you know how to code in MATLAB there are some functions in SPM that could help. Essentially, you could do something similar to the following...
>
> P=spm_select(2,nifti,'Select DTI and AAL');
> V=spm_vol(P);
> V(2).mat = M*V(2).mat; % where M is the appropriate matrix.
> spm_reslice(V,struct('mask',false,'mean',false,'interp',0,'which',1,'wrap',[0 0 0],'prefix','r'));
>
> Best regards,
> -John
>
> 2012/1/1 ÀîÎÀÄÈ <[log in to unmask]>
>
> Dear friends,
>
>
>
> I have the transformation matrix from MNI space to DTI space, is there anyway that I can transform the AAL template to DTI space by spm8?
>
>
>
> Thank you and happy new year.
>
>
>
>
>
> Weina
>
>
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>
>
>
>
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