Using -act argument to tcksift2 in qsirecon?

kjamison · October 2, 2026, 5:35pm

I only recently realized that tcksift2 has the -act <5ttvol> option and that it seems to be recommended, particularly when -act <5ttvol> was used for tckgen. I can confirm that the sift2 weights are different when using tcksift2 -act … . Am I correct in suggesting qsirecon currently has no way to run tcksift2 with -act?

I’m not certain what the right answer is for using it or not, but it seems like it is worth having the option, and worth discussing as far as default pipelines go?

Steven · October 2, 2026, 6:04pm

Hi @kjamison,

QSIRecon should employ the ACT for Sift2.

github.com/PennLINC/qsirecon

qsirecon/interfaces/mrtrix.py

07a68649a


      
          class SIFT2InputSpec(MRTrix3BaseInputSpec):
              in_tracks = File(argstr='%s', exists=True, mandatory=True, position=-3, desc='input tck file')
              in_fod = File(argstr='%s', position=-2, exists=True, mandatory=True, desc='input FOD SH file')
              out_weights = File(
                  argstr='%s',
                  position=-1,
                  genfile=True,
                  desc='output text file containing the weightingfactor for each streamline',
              )
              act_file = File(
                  exists=True,
                  argstr='-act %s',
                  desc=(
                      'use the Anatomically-Constrained Tractography framework during'
                      ' tracking; provided image must be in the 5TT '
                      '(five - tissue - type) format'
                  ),
              )

github.com/PennLINC/qsirecon

qsirecon/workflows/recon/mrtrix.py?plain=1

26.0.1


      
          if use_5tt:
              workflow.connect(inputnode, connect_5tt, tck_sift2, 'act_file')

Have you looked at the working directory to see if it is included in the command?

Best,
Steven