Hi Saad,
I'm running tractography from the GM-WM boundary with the --omatrix1 flag and the pial surface (converted to volume) as a stop mask (as you recommended in an earlier post) to obtain a whole-brain connectivity matrix.
I would like the streamline to terminate as soon as it reaches the seed/target mask, such that the sum of a row in the connectivity matrix doesn't exceed the number of streamlines (given that the diagonal of the connectivity matrix is subtracted). As it is now the streamlines continue along the seed mask and makes it possible for a single streamline to connect a seed to multiple targets. Is there a way to avoid this? I have also tried to use the seed mask as termination mask, but this results in termination of the streamlines before they leave the seed mask.
Another question, just to make sure I got it right. Is it possible to parallelize probtrackx2 by choosing different --rseed and sum up the results in the end?
Best,
Karen
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