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
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