Hi
You can save the individual streamlines in probtrackx2, but this is more of a “debug” option, as the streamlines are saved in a very sub-optimal fashion as an ascii text file. We never encouraged looking at individual streamlines because they are noisy samples from a distribution, so we prefer to look at the distribution itself.
The fdt_coordinates.txt file referred to in the practical is not what you are after. That file simply saves the seed coordinates in the case where the seed is provided as coordinates, as opposed to a voxel mask.
The option to save out tract coordinates is hidden. It is the —savepaths option.
Cheers
Saad
> On 7 Feb 2020, at 22:47, James Andrew Taylor <[log in to unmask]> wrote:
>
> Hello!
>
> I'm used to using deterministic tractography and having a streamlines file to visualize. Is there no way to keep the generated fibers file using probtrackx? If there's any confusion, I'm referring to what would be .trk or .tck files with DSI Studio or MRtrix -- lists of coordinates indicating the path each fiber took. In the FDT tractography practical (https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt2/index.html), an output of probtrackx called fdt_coordinates.txt is mentioned -- I don't get this output when I run probtrackx. I wonder if that's what I'm looking for.
>
> Sorry if I'm somehow misunderstanding how probabilistic tracking works!
>
> Thanks for reading,
> -James Andrew Taylor
>
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