Dear Tim,
Thanks very much for your reply. It is very helpful.
Jian
________________________________
> Date: Tue, 1 Jul 2008 20:03:18 +0100
> From: [log in to unmask]
> Subject: Re: [SPM] Scaling factor from Normlisation & et
> To: [log in to unmask]
>
> Dear Jian,
>
> I'm not sure where the cube root comes in, but I can already see two problems: One, you need to use the *_inv_seg_sn.mat file, as the *_seg_sn.mat file doesn't have an informative Affine transformation; Two, you have to account for the possibly different voxel sizes in the object and template images, as stored in the VF.mat and VG.mat transformation matricies.
>
> While John's help, I wrote the following code to find the affine-related volume change from a SPM5 spatial normalisation:
>
> p=load('myimage_inv_seg_sn.mat');
> Aff_NativeToAtlas = det(p.VF(1).mat*p.Affine/p.VG(1).mat);
> Aff_AtlasToNative = 1/Aff_NativeToAtlas;
>
> As a sanity check, you should generally find that Aff_NativeToAtlas is slightly larger than one, as the atlas is larger than the average brain.
>
> -Tom
>
>
> On Tue, Jun 24, 2008 at 7:24 AM, jian chen wrote:
> Dear List,
>
> I have two questions about the matrix obtained from segmentation/normlisation in SPM5.
>
> 1. I have read before in the list it says the spatial scaling factor in the normalisation process can be obtained by cubed square root of determinant of Affine element in the *sn.mat. For one of my image I had:
>
> load sDLPFC10-0031-00001-000160-00_seg_sn.mat
> det(Affine).^(1/3)
>
> ans =
>
> 3.2254
>
> It looks very big to me and I even had something over 4 for other images. Is it right?
>
>
> 2. Is there any way to apply *sn.mat to a single voxel coordinate in the native space image to get the coordinate in normalised space (this is the same image that was used to obtain the *sn.mat file)?
>
> Thanks in advance for any help.
>
> Jian
>
>
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre
_________________________________________________________________
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