Ali Ghayoor

@ntustison : Hi Nick, please review this PR. Hope it helps the ants community.

@cookpa : It generates less confusion. For example when you want to skip just one middle step of antsCorticalThickness. Can you skip only step "5: DiReCT cortical thickness" and run...

Yes, it basically removes the step "5: DiReCT cortical thickness" and trims the code and the command line so it is only dedicated to segmentation.

Hi @ntustison , I think we can add developments to antsCorticalThickness pipeline, so it can skip a specific stage. However, it was my preference to make a dedicated pipeline for...

Hi @mattcieslak , Do you have any idea about the issue reported here? Also, I am interested to get the colorFA, which of the default `recon_spec`s do you recommend to...

Hi, bvals are exactly the same, but bvecs are in opposite directions. Also, bvecs are different from the 3rd number after the decimal point.

Here is bvecs for run1: > 0 -0.203737 -0.198274 -0.402136 -0.404018 -0.202985 -0.854935 -0.730935 -0.406286 -0.73048 -0.652278 -0.323539 -0.324763 -0.650725 -0.979138 -0.854525 -0.00141114 -0.00315668 -0. 653786 -0.329346 -0.198481 -0.203793 -0.652591...

Thanks @mattcieslak , I used `--distortion-group-merge concat`, and I got a different error message: > Node: qsiprep_wf.single_subject_01_wf.sub_01_final_merge_wf.distortion_merger > Working directory: /tmp/work/qsiprep_wf/single_subject_01_wf/sub_01_final_merge_wf/distortion_merger > > Node inputs: > > b0_refs = >...

@cookpa , please update us on the results with `average`. I ran this option on PPMI data, and reported the error above (It couldn't find the DWI pairs).

Hi @mattcieslak , I wanted to follow up here to see if you have any idea about the above error when `concat` is used? Thank you!