I am trying to run SIFT2 on a tractogram not obtained with MRtrix. This means I had to convert my tractogram to tck file format using tckconvert. The problem is that tckconvert does not write step size information into the tck header and thus SIFT2 is not able to process the data. Is there an elegant way to hack the step size information into the tck header?
UPDATE: I modified the header manually by inserting the line “step_size: 0.2” and adjusting the header size info accordingly, but while being able to do something with it, SIFT2 seems to be producing a lot of nan values.
UPDATE 2: Apparently it was an RAS-LPS issue. Flipping the fibers did the trick. So I guess only the second question below is still open
My second question is about the SIFT2 output. If I got it correctly, SIFT2 generates an artificial FOD image from the weighted input fibers to explain the given FOD image in the best possible way. Is it possible to output the “unexplained” parts of the FOD image?