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Subject:

Re: reverse normalisation help

From:

Marko Wilke <[log in to unmask]>

Reply-To:

Marko Wilke <[log in to unmask]>

Date:

Tue, 14 Oct 2008 09:19:03 +0200

Content-Type:

text/plain

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Parts/Attachments

text/plain (57 lines)

Hi Richard,

> Bear with me - I am a novice....

We all either are or were :)

> I realise there is a code for reversing the linear affine components 
> (although I have yet to track it down) but I am also wondering whether 
> there is now a way in which the nonlinear component can be reversed.

Yes, by segmenting the image in SPM5 (quite counterintuitive, I know). 
During this procedure, a "spatial normalization" mat file will be 
generated, as well as the inverse of that. This will do what you want, 
as described by John on July 31:

> If you used the Segment button in SPM5, then there will also be a 
> *_seg_inv_sn.mat file (as well as a *_seg_sn.mat).  You can use this to do a 
> "Write Normalised".  If you set the bb to nan(2,3) and the voxel size to 
> nan(1,3), then the dimensions of the inverse normalised image should be 
> (about) the same as those of the image from which the parameters were derived 
> from.
> 
> If you didn't use the Segment button, then the Deformations utility of SPM5 
> can be used for taking a *_sn.mat file, inverting it and writing an inverse 
> normalised image.  The SPM5 manual should give you a few clues.
> 
> Best regards,
> -John

Just one more thing:

> and then adjust the position manually, however, our concern is that the 
> linear components are least effective in our area of interest (which is 
> the temporal pole) and we infact need the non-linear component.

The overall scaling that is occurring in the image is quite dominated by 
the linear scaling. If you look at John's paper from 1997 
("Incorporating prior knowledge...") you will see that by the affine 
component alone, the image is scaled by about 1.4. Regional or local 
effects of the non-linear normalization interfere, and I agree that a 
combined approach is better. However, if you look at images that are 
normalized using an affine-only approach, you will be surprised how well 
they are registered to the template already (at least I was :)

Best,
Marko
-- 
=====================================================================
Marko Wilke                                            (Dr.med./M.D.)
                 [log in to unmask]

Universitäts-Kinderklinik              University Children's Hospital
Abt. III (Neuropädiatrie)             Dept. III (Pediatric neurology)
             Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416                   Fax: (+49) 07071 29-5473
=====================================================================

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