Converting nifti file into tck tract format

Dear all,

I’ve run probabilistic tractography using the FSL probtrackx2 tool. So I ended up with a nifti file as result and I look pretty good to me. However I would like to convert the nifti file output to .tck format.
Do you have any suggestion?

Thanks in advance


That can’t be done: your NIfTI image is presumably basically a track density image, it’s not possible to go back from that to the original streamlines data. I’ve no idea whether it’s possible to get probtrackx2 to output the actual streamlines data…(?)

It is possible to get probtrackx to output streamlines, there is a hidden flag (-savepaths I think).

However, the FSL group explicitly state that it should only be used for debugging.

From reading fora, the streamlines are output as txt files and if too many are called the program tends to crash (once again if memory serves).