Hi Ana,
yes, I would define my seeds in standard space. In probtrackx2 you can then provide the warp fields as input to map those seeds to diffusion space.
When you have your dense matrix1 output, you can normalise it using the waytotal.
Hope this helps, cheers,
Matteo
> On 27 Feb 2018, at 10:21, Ana Coelho <[log in to unmask]> wrote:
>
> Thanks! Those materials where really helpful.
> Another question, I want to build the voxel-wise structural connectomes for different subjects so I should use seeds in standard space or seeds in subject diffusion space and then transform the results to standard space?
> Also, how can I normalize the voxel-wise matrix? I know that for ROI to ROI matrix we use waytotal file, but for a voxel by voxel matrix what is the best method?
>
> Best regards,
> Ana
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