Stefano,

I am afraid, no. In SPM5, segmentation involves the procedure previously
called "optimised VBM" and thus is able to create both transformations. In
general, segmentation in SPM5 seems to be superior to the old-style
normalisation method.

Volkmar

On Wed, 15 Mar 2006, Marenco, Stefano (NIH/NIMH) [E] wrote:

> Is it possible to automatically save the inverse normalization
> transformation matrix using the normalization button (rather than the
> segmentation button) in spm5?
>
> Stefano Marenco, MD
> GCAP, Clinical Brain Disorders Branch,
> NIMH
> 10 Center Drive, room 4S235
> Bethesda, MD 20892
> tel. (301) 435-8964
> fax. (301) 480-7795
> email: [log in to unmask]
>
>
> -----Original Message-----
> From: Volkmar Glauche [mailto:[log in to unmask]]
> Sent: Thursday, March 09, 2006 7:23 AM
> To: [log in to unmask]
> Subject: Re: [SPM] contrast coregistration to a (wfu_pickatlas) mask
>
> If you use SPM5s "segment" to create the normalisation parameters, you
> will also get the inverse parameter set which will map from MNI to
> individual coordinates. The only thing to to is then to "write
> normalised"
> the MNI space ROI using the *_inv_sn.mat file from each individual
> subject.
>
> On Wed, 8 Mar 2006, Joseph Maldjian wrote:
>
> > Kelly,
> >
> > The pickatlas generates ROIs in MNI space. If you want to use the
> > pickatlas ROIs in native space, you need to be able to apply an
> > appropriate transformation matrix defining MNI -> native space.
> > Although the information for this transformation exists in your
> > normalization sn.mat file combined with your coregistration
> > transformation matrix, SPM will not directly perform the reverse
> > normalization procedure. There has been code posted by John Ashburner
> > that allows you to compute the reverse normalization transformation
> that
> > takes into account any deformation fields in the normalization.
> > You would have to apply this "inverse" normalization matrix to the
> > pickatlas ROI, and then apply the inverse coregistration matrix from
> > your step 5 to the ROI.
> >
> > Sounds bad, but that's part of the price for trying to use native
> space
> > with normalized ROIs. Someone out there may already have some useful
> > code that does all this. We have a program that does the reverse
> > normalization based on only Affine transformations (ignores
> deformation
> > fields).
> >
> > Hope this helps
> >
> >
> ------------------------------------------------------------------------
> > ----------
> > Joseph A. Maldjian, MD
> > Professor, Dept. of Radiology and Biomedical Engineering
> > Director Advanced Neuroscience Imaging Research Core (ANSIR)
> > Wake Forest University School of Medicine
> > Office: 336 716-2815
> > fax: 336 716-2870
> > email: [log in to unmask]
> > website: www.ansir.wfubmc.edu/maldjian.htm
> > <http://www.ansir.wfubmc.edu/maldjian.htm>
> >
> ------------------------------------------------------------------------
> > ----------
> >
> >
> >
> > -----Original Message-----
> > From: SPM (Statistical Parametric Mapping)
> > [mailto:[log in to unmask]] On Behalf Of Kelly Diederen
> > Sent: Wednesday, March 08, 2006 8:51 AM
> > To: [log in to unmask]
> > Subject: [SPM] contrast coregistration to a (wfu_pickatlas) mask
> >
> >
> > Dear researchers,
> >
> > I analyzed my data using the following procedure:
> >
> > 1 realignment
> > 2 statistics
> > 3 estimation
> > 4 results
> > 5 coresgistration of the contrasts to the anatomical image
> > 6 normalization of the coregistered contrasts to the T1
> > template.
> >
> > I decided to normalize the contrasts at the end of the procedure
> > to enable myzelf to look both at the normalized and non-normalized
> data
> > without doing two separate analysis'.
> >
> > Next to this I made a mask with the WFU_pickatlas in order to
> > visualize the ROI's for further analysis. Since the pickatlas
> generates
> > normalized masks I can't use in the results section since my data
> aren't
> > normalized yet. Thats why I tried to coregister the masks with the
> > contrasts after step 6.
> > However this doesn't work, whichever way I tried it.
> > Is there a way to do this with the pickatlas without normalizing
> > the scans before the estimation (and without coregistration of the
> mask
> > with the functional scans before the estimation part)?
> >
> > Thank you in advance,
> >
> > Kelly Diederen
> >
> >
> >
> >
> >
>
>

--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg