Hi
Yes and no.
You can use the matrix2 option to seed from the whole white matter and use the grey matter as a target. That will output a big WMxGM matrix. Given two ROIs on the cortex you can extract two sets of columns which represent the white matter connecting to those ROIs. The intersection of the two is then the WM pathways that connect to both ROIs. However you can imagine situations where, from a given voxel, streamlines going to one or the other ROI may be doing so through different crossing fibre orientations. So this way of defining the pathways is not as accurate as actually streamlining between the two ROIs. The same reasoning applies if you seed from the whole GM and define the WM as a target.
Cheers
Saad
> On 15 Aug 2019, at 19:28, Aldana Lizarraga <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I'd like to run probabilistic tractography in the whole brain, independently of any grey matter parcelation. For instance, choosing the grey matter as target mask, and white matter as the seed mask.
>
> Is it possible after that to define ROIs to isolate the paths that connect them?
>
> Best regards,
>
> Aldana
>
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