> I am using a mask for my region of interest. And my question was about multiplying this mask by the sienax grey matter mask in order to have better alignment of my mask (ROI) and also to avoid having my mask encroach onto the white matter since my aim is to assess the connectivity.
> So, I was actually wondering if this step is necessary?
This still isn't entirely clear to me, but if you are using an ROI to investigate white matter then multiplying by a SIENAX brain mask will be fine (but have no effect, most likely). However, multiplying by a grey matter mask, if the ROI is not grey matter would be bad. If the ROI is grey matter, then this multiplication would be helpful (to eliminate white matter and CSF from the mask).
> But now I have problems with the mask itself since it's not well aligned to my region of interest.
I'm not sure if you mean the mask of your region of interest or the sienax mask.
> Since this is not a manual mask, I am not able to change anything. Do you have any suggestions regarding this problem?
I don't fully understand what is what, so it is difficult to answer. If you have masks in different spaces (e.g., associated with diffusion images, or the MNI space, or the T1/anatomical image space) then you need to transform the masks into a consistent space. Or, if you are using the FDT GUI then you can just specify what space the mask is in and then give it an appropriate transformation (derived from registrations between the spaces in question). If you want to multiply images then they must be in the same space and you would need to use the transformations (derived from registrations) and apply these to resample/transform the mask from one space to another. For example, use applywarp to shift an image from the MNI space to the anatomical space, using the appropriate warp (from standard to structural space).
> And regarding multiplication of mask with the sienax pve_1 grey matter, do you recommend it?
I would not recommend multiplying by a non-binary mask (like a PVE).
> I hope I did not cause more confusion. Thanks.
I'm still a little unclear about details, but hopefully the above will help you.
All the best,