Hi, Ellen-
Glad you found the root of the different matrix problem.
The pipeline I use and recommend for distortion correction, tensor estimation, and more is the AFNI+TORTOISE+FreeSurfer pipeline described in the FATCAT_DEMO2 here:
[
afni.nimh.nih.gov]
It goes from start to finish with processing. The TORTOISE tools DIFFPREP and DR_BUDDI perform Gibbs ringing+motion+eddy current distortion correction and EPI distortion correction, respectively. (Performing EPI distortion correction with DR_BUDDI depends on having a dual phase encoded DWI acquisition.)
I am obviously biased, but I think the FATCAT_DEMO2 describes a good road to be on.
Tying with your previous question:
Re. converting FreeSurfer output to NIFTIs and GIFTIs: yes, I would use @SUMA_Make_Spec_FS. That is part of the FATCAT_DEMO2 pipeline. All the outputs from there get brought to diffusion space in the demo pipeline.
I am not familiar with the Nipype align tool, or what it does exactly with diffusion data, unfortunately.
--pt