Hi Andreas,
what happens if you explicitly specify voxel sizes and bounding box
instead of setting them to NaN? What is the orientation of your template
slices?
Volkmar
On Wed, 3 Jan 2007, Andreas Bruns wrote:
> Hi Philipp,
>
> thank you for your comments, and sorry for being unclear about the
> processing stream. Actually, I do NOT perform any segmentation before
> normalisation (it is just a *_sn.mat file, not a *_seg_sn.mat file), since
> I am analyzing data from small rodents, for which I do not have tissue
> probability maps (and no experience so far as to which tissue types would
> be suitable for segmentation, anyway).
>
> So -- are there any other ideas?
>
> Thanks again,
>
> Andreas
>
>
> ----------------------
>
> Biozentrum of the University of Basel
> Klingelbergstrasse 50/70
> 4056 Basel
> Switzerland
>
> =========================================================================
>
> On Tue, 2 Jan 2007 17:47:53 +0100, Saemann Philipp
> <[log in to unmask]> wrote:
>
>> Hello Andreas,
>>
>> I do not know if this effects would appeaar if you use the combined
>> segmentation/normalisation routine from SPM5 (which gives you *seg_sn.mat
>> files).
>> It was not entirely clear from your mail how you have gained the *sn.mat
>> files (i. e from
>> the segmentation or the normalisation routine).
>>
>> If it is *seg_sn.mat" files you may try the VBM toolbox function "write
>> segmentation only",
>> which is the equivalent to "write only" of earlier SPM versions or the SPM5
>> normalize function.
>>
>> Download from:
>>
>> http://dbm.neuro.uni-jena.de/vbm
>>
>> However, programmers may have additional ideas on your question.
>>
>> best regards,
>> Philipp
>>
>>
>> Max-Planck-Institute of Psychiatry
>> NMR Research Group
>> Kraepelinsr. 2-10
>> 80804 Munich
>> Mail: [log in to unmask]
>> Phone: 0049-89-30622-413
>> =========================================================================
>
>
> On Tue, 2 Jan 2007 16:22:45 +0000, Andreas Bruns <[log in to unmask]>
> wrote:
>
>> Dear SPMers,
>>
>> applying a *_sn.mat file to an image involves explicit resampling by means
>> of the "Normalise: Write" option or the "Deformations" utility. When using
>> nan(1,3) for the voxel size and nan(2,3) for the bounding box, the
>> dimensions of the template image are used, BUT with a slight tolerance, so
>> that in general, there is no exact one-to-one (voxel-by-voxel) mapping
>> between the template and the normalised image. Instead, I repeatedly
>> obtained a 1-voxel discrepancy in image size and/or a half-voxel offset
>> between the images in one or more direction(s).
>>
>> Certainly, these differences are well accounted for by the information in
>> the header file, so that the images are correctly co-registered. Still, if
> I
>> want to have perfect spatial correspondence between the images, I need an
>> additional resampling step for the normalised image by means of, e.g., the
>> "ImCalc" feature. This requires about twice as much time and disk space,
> and
>> (what is worse) it introduces more smoothing due to the additional
>> interpolation step.
>>
>> Is there a way to avoid the double resampling and directly tell the
>> "Normalise: Write" or "Deformation" (or any other) module(s) to use not
> only
>> the same voxel size and bounding box as in the template (or even better: in
>> any arbitrary) image, but even the very same voxel positions and image
>> dimensions?
>>
>> Thank you very much in advance,
>>
>> Andreas
>> ========================================================================
>
>
--
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 http://fbi.uniklinik-freiburg.de/
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