Hi
Sorry for not replying to this. We will try to look into these differences between the CPU and GPU you mention.
Note however : when you specify mutiple —avoid options (or any other options), it is the last one that is considered and all others are ignored by the program.
Cheers
Saad
> On 17 Oct 2019, at 20:26, Matthias Heyne <[log in to unmask]> wrote:
>
> Update:
> The probtrackx2 non-GPU version (also) doesn't seem to apply the second stop mask if multiple ones are supplied via a text file; however, it's still surprising that GPU and non-GPU versions of the tool would produce different (incorrect) outputs.
>
> On the other hand, it seems possible to constrain tracking by supplying a white matter surface mask (either as gifti surface or nifti volume) and specifying it as an additional avoid mask; this is even possible by including multiple --avoid=xxx flags (without having to generate an additional text file listing both). Note that using a surface file still requires the meshspace=[caret/freesurfer] and seedref=[volume] flags.
>
> Happy tracking!
> Matthias
>
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