Dear Sebastian,
This issue is really nothing to do with setup_masks per se and really just about what to do with transformed lesion masks in general. I would say that the safest thing to do in this case is to make sure that you exclude the lesions from your calculations, and so you should transform the masks (getting values between zero and one) and then threshold and binarise them. I would choose a threshold near zero, so that you exclude voxels in the 2mm space that have anything more than a minor overlap with the lesion masks in the 1mm space. A threshold of say 0.1 would be appropriate. The analysis would then continue in such a way that only 2mm voxels that had less than a 10% overlap with the lesion mask would be included in the analysis. This would be true whether you used setup_masks or not.
I hope that helps.
All the best,
Mark
On 28 May 2013, at 09:47, Sebastian Papazoglou <[log in to unmask]> wrote:
> Dear Experts,
>
> I have an issue with setup_masks.
>
> We built a VBM template using customised versions of the scripts fslvbm_2 and 3 that account for lesion masks.
> The resolution of the original data is 1mm iso. During registration to standard space the resolution is downsampled to 2mm.
> Hence we will also have to coregister our lesion masks correspondingly in order to generate proper regressor images
> using setup_masks.
>
> Would you recommend using the interpolated lesion masks (values between zero and one) as input to setup_masks-
> or is it mandatory to use thresholded "binary" masks?
>
> Many thanks in advance.
>
> Best regards,
> Sebastian
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