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Subject:

Re: Optimal setting for VBM/asymmetry measures

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Wed, 15 Feb 2012 10:54:22 +0000

Content-Type:

multipart/mixed

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text/plain (49 lines) , cg_lat_index.m (49 lines)

Dear Gabor,

in order to perform an asymmetry analysis in VBM you have to use a symmetrical template. The symmetrical template that I provide with my toolbox can be used for that purpose and should be selected as TPM image in VBM8. However, it is not possible to use DARTEL because the provided DARTEL template is not symmetric and there is no easy way to do this. Thus, you have to deselect the DARTEL option in VBM8.
You can use the attached tool to calculate the lateralization index.

Regards,

Christian



On Fri, 27 Jan 2012 14:45:13 +0000, Gabor Oederland <[log in to unmask]> wrote:

>Hello,
>
>
>I used the current version of VBM8 (r435) for segmentation (standard parameters including high-dimensional DARTEL). Now I'm trying to calculate asymmetry measures for VBM data based on the differences between the preprocessed orignal images and their flipped counterparts using the fomula (orig – flip)/(0.5*(orig+flip) as proposed e.g. by Luders et al. (2004).
>
>I had a look at the literature, the papers slightly differ in the way they preprocess the images. Derflinger et al. (2011) use normal routines but a symmetric template (TPM?) and then flip the modulated normalised images. For asymmetry measures, they create difference images with the formula above. But this should actually mean that the difference images are not in MNI space anymore, due to the symmetric templates.
>In contrast, Takao et al. (2011, Hum Brain Mapp) simply subtract the flipped from the original image. Then they normalise the group-specific symmetric grey matter template onto the asymmetric gray matter template and use these parameters to normalise the differential images as well.
>
>
>Now I was wondering what the "perfect" way would be. First off, I only have a small group of 25 subjects. In this case it seems not to be recommended to create group-specific TPMs (BTW, would it still be possible or is it just wrong?), so I have to use some symmetric TPMs from other studies.
>
>The author of the VBM8 toolbox, Christian Gaser, provides a symmetric TPM file at http://dbm.neuro.uni-jena.de/vbm8/ Now I'm wondering,
>
>a) this template is not in MNI space, so should I later on normalise this template onto the standard TPM file as proposed by Takao et al. and then the differential GM images? As far as I understood the TPMs are used for initial normalisation only in VBM8, but this should have an effect though? Or is a potential bias corrected by warping onto the DARTEL template included in VBM8?
>b) It seems that the T1.nii template as included in SPM8 is used for some initial steps during the preprocessing pipeline in VBM8. So is there a need for a symmetric T1 template? 
>c) when using VBM8 (or any other) symmetric TPM file for the first segmentation, I should use a symmetric DARTEL template as well, shouldn't I? Is such a file around or would it be ok to simply create a mean image out of the DARTEL templates provided with VBM8 and its flipped versions? 
>
>Finally, with increasing voxel size, now 1.5x1.5x1.5 mm in VBM8, would it be good to correct for the difference between origin and midline (about 0.7 mm along x axis = right-left) before flipping? I understand that it does not make that much sense with low-resolution fMRI data, but for VBM8 data the misplacement is about half of a voxel size.
>But this would mean to reslice the images, right? As far as I can see none of the VBM papers has dealt with that topic so far (at least they only refer to "flipping" without any further details). Some of them explicitly state that the images were flipped at x = 0 though. There's a PET stuy by Didelot et al. (2010) which mentions the misplacement but does not correct for either.
>
>
>Thanks for any comments!
>
>
>Gabor
>
>
>Quotes
>
>Deflinger et al. (2011). Grey-Matter Atrophy in Alzheimer’s Disease is Asymmetric but not Lateralized. Neuroimage
>Didelot et al. (2010). Voxel-Based Analysis of Asymmetry Index Maps Increases  the Specificity of 18F-MPPF PET Abnormalities for Localizing the Epileptogenic Zone in Temporal Lobe Epilepsies. J Nucl Med
>Luders et al. (2004). A voxel-based approach to gray matter asymmetries. Neuroimage
>Takao et al. (2011). Gray and White Matter Asymmetries in Healthy Individuals Aged 21–29 Years: A Voxel-Based Morphometry and Diffusion Tensor Imaging Study. Human Brain Mapping


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