Hi everyone,
I’m using MRtrix3 (version 3.0.3) and I would appreciate some advice on handling invalid DTI values when sampling diffusion metrics along streamlines.
I have already performed tractography using iFOD2 with ACT, followed by SIFT2. I then fitted the diffusion tensor using dwi2tensor and calculated FA, MD, AD and RD using tensor2metric.
However, some voxels have negative values for these metrics, or FA > 1, presumably due to negative tensor eigenvalues.
I would prefer not to clip these values or replace negative eigenvalues with zero.
My goal is to calculate the mean FA, MD, AD and RD along each streamline using tcksample, and subsequently construct connectomes using these streamline averages.
My questions are:
- What is the recommended approach for dealing with voxels containing negative tensor eigenvalues or physically invalid DTI metrics?
- Is there a simple way in MRtrix to ignore specific voxels when calculating the mean along a streamline? Ideally, I would like to retain the valid portions of each streamline and exclude only the invalid voxel contributions, without treating them as zeros or discarding the entire streamline.
Thanks in advance for your help!