SIFT 2 pathway of interest

Dear MRtrix experts,

I am sorry for the question, I am new using Mrtrix. I processed a whole brain tractogram with a combination of SIFT and SIFT2. Now, I want to extract a pathway of interest (to quantify streamlines) from the whole tractogram filtered by SIFT. Additionally I have the txt file provided by SIFT2 with the weights of the streamlines.

How should I use the information provided by SIFT2 to extract a pathway of interest with meaningful streamlines?

Thank you


Hi Josue,

Generally there’s two ways that this type of experiment would be performed:

  1. Extraction from a connectome
    If your pathway of interest is simply one edge (or a small set of edges) within a connectome representation, then you can simply generate the connectome (ensuring that you also provide the SIFT2 streamline weights to the tck2connectome command), and then identify the element(s) within the connectome matrix that correspond to your pathway of interest.

  2. Manual extraction
    The tckedit command can be used to “edit” track files, e.g. by retaining some streamlines and removing others. This requires manual definition of whatever criteria you wish to apply to extract your pathway of interest from the whole-brain tractogram. The trick here is to use the -tck_weights_in and -tck_weights_out options in tckedit; this will provide you with a SIFT2 weights file intended to accompany the track file produced by tckedit, which contains the weights as calculated by SIFT2 of only those streamlines present within the pathway of interest.

Hope one of these two serves your purposes!


Thank you so much Rob!!