julie

I'm running into the same "index X is out of bounds for axis 2 with size X". I managed to trace the error but maybe someone can elaborate on what's...

Hi @wasserth - glad the detailed analysis helps! I did a bit more digging and, unfortunately, I don't think your code addresses the root issue that I'm having: * The...

Re: the original mask_path error, I narrowed it down to the path building [line 268 in `plot_tractometry_results`](https://github.com/MIC-DKFZ/TractSeg/blob/master/bin/plot_tractometry_results#L268). It joins the `plot_3D` path in `subjects.txt` (i.e., the `tractseg_output` folder) with `../nodif_brain_mask.nii.gz`....

> Has there been any progress fixing this issue? Or a workaround? @jdias001 - I'd suggest eroding the `brain_mask.nii` file by 1 voxel (e.g., with MRtrix3's maskfilter) and using `mrmath`...