Dear Mr. Gaser,
I have some additional questions on the new VBM8 Toolbox.
1. Which tissue-types are used for the Dartel-normalisation? 
2. How are the Jacobians modulated? Am I right in assuming that the initial affine transformation to MNI space is used for that normalisation and hence does not involve non-linear components? If so, is there a possibility to get unmodulated jacobians in MNI space, so that global head size is already accounted for?

Thanks for this very helpful toolbox.

Best regards,
Michel Grothe

> Date: Sun, 16 May 2010 23:15:18 +0100
> From: [log in to unmask]
> Subject: Re: [SPM] Beta Version of VBM8 Toolbox
> To: [log in to unmask]
>
> Dear Paul,
>
> > Thanks for your toolbox. I have some questions about parameter setting
> >
> > 1. How to change DARTEL export image voxel size, i think the default setting about DARTEL export image is 1.5 cubic
> The voxel size is always set to the voxel size of the tissue probability map (TPM) image. However, if you don't need a customized Dartel template you can use the Dartel approach, which is integrated in VBM8. This Dartel approach will use the Dartel MNI template provided with VBM8 and no additional export or Dartel use is neeeded.
>
> >
> > 2. How to change HMRF weighting ?
> > (In VBM5, we can choose different HMRF weighting in GUI. If i want to use iterative HMRF weighting, how can we choose in this version?)
> In VBM8 two de-noising techniques are used. The first is a non-local means filter as preprocessing step. The filter size is automatically estimated based on the local variance of your image. The second is a MRF, which is integrated in the segmentation process. Again the weighting is now internally estimated based on the noise in your image. However, both approaches can be weighted. The non-local means filter is by default weighted by 0.7, which shows best performance for segmentation. The weighting for the MRF is fixed to 0.15. Both values are optimal for a large variety of data and usually it is not necessary to change the weighting. The weighting can be rather used to deselect the filter by setting the weighting to 0. Anyway, I have now added the option to change both weightings. This will also solve some problems with batch files, where changes of these parameters in cg_vbm8_defaults.m were not considered. Thanks to Jose V. Manjon for pointing to that problem.
> The new version can be downloaded at:
> http://dbm.neuro.uni-jena.de/vbm8/vbm8_r331.zip
>
> Or simply use the update function in VBM8.
>
> Regards,
>
> Christian
>
> ____________________________________________________________________________
>
> Christian Gaser, Ph.D.
> Assistant Professor of Computational Neuroscience
> Department of Psychiatry
> Friedrich-Schiller-University of Jena
> Jahnstrasse 3, D-07743 Jena, Germany
> Tel: ++49-3641-934752 Fax: ++49-3641-934755
> e-mail: [log in to unmask]
> http://dbm.neuro.uni-jena.de
>
> >
> > Best
> >
> > Paul


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