Hello,
Without knowing the numerical format of both the VTA atlas and your existing ROI mask, it is hard to definitively say if this will be a problem. In general most FSL tools treat masked voxels as those with a intensity > 0.5. A safe pre-processing step is to binarise a mask before applying it to data.
Kind Regards
Matthew
> We recently acquired a probabilistic atlas of the VTA from another researcher. We added it to my existing ROI mask using fslmaths. When we open the resulting ROI mask in FSL-View, the VTA seems to show up at a different baseline intensity value than the rest of the areas in the mask. The other areas were derived from the Harvard-Oxford atlases implemented in FSL.
>
> Is this a problem for analysis (specifically, using this for "pre-threshold masking" in FEAT), and if so, is there anything I can do to fix it?
>
> Thank you,
>
> Peter
|