On Wed, 11 Dec 2013 14:12:08 +0000, Michel Grothe <[log in to unmask]> wrote:
>Dear Christian (or anyone else eager to answer ;-)),
>I was wondering which kind of SPM "standard" normalisation the VBM8 toolbox uses when changing the normalization settings from "high-dimensional DARTEL" to "SPM low-dimensional"? Old-fashioned "Normalise"-Button or the one in SPM5-style unified segmentation?
It's the normalization that is used in the unified segmentation approach ("New segment") in SPM8.
>I noticed that the TPM-file where images are normalised to in the case of "low-dimensional" normalisation is taken from the "New segment" toolbox, meaning that it includes a total of 6 tissue-types. Are all parts of this TPM-file used for matching the tissue-segments, or just the GM and WM (and CSF?) partitions.
Only GM and WM are used for normalization. All other classes are only used as prior for the segmentation.
If I wanted to include my own TPMs, would it be sufficient to specify a TPM-file with just the 2 volumes for GM and WM? The manual recommends using the TOM toolbox, but I already have mean GM and WM maps of an independent study population (actually a DARTEL template), which I would like to use.
No, this will not work, because the priors for segmentation are necessary.
>Similarly, if I wanted to compare directly the outcomes from "high-dimensional" vs "low-dimensional" normalization strategies, I would like to ensure that the reference template is identical for the two approaches. Thus, would it be reasonable to replace the default TPM-file with the GM and WM partitions from the DARTEL-IXI-template (_6), or would you recommend a different approach? I know, the TPM-file and the IXI segments should be analogue because both are in MNI space, but still...
Because the spatial normalization is working so different a direct comparison using the same template will not work. The standard normalization (from new segment) will use GM/WM of one template (TPM.nii). In contrast Dartel needs templates for each iteration step with increasing spatial accuracy. The Dartel-template that is provided with VBM8 (or for any other template that you obtain after creating a customized template using Dartel) contains of 2 tissues classes (GM/WM) and 6 iteration steps.
>Thanks in advance for your help.