Just to follow up on @Steven’s post: technically QSIRecon expects atlases to follow an older version of the BEP. BIDS has since merged the BEP with some changes, so QSIRecon expects something that isn’t actually BIDS-compliant.
Here is an example tree from a test:
/path
├── atlas-carpet
│ ├── atlas-carpet_space-MNI152NLin2009cAsym_dseg.json
│ ├── atlas-carpet_space-MNI152NLin2009cAsym_dseg.tsv
│ └── atlas-carpet_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz
└── dataset_description.json
In the dataset_description.json, you should have DatasetType set to atlas. Since, in that example, the atlas dataset is located at /path and the name of the atlas (from atlas-<label>) is carpet, you could pass that in as --datasets carpet=/path --atlases carpet.
We plan to overhaul atlas organization to match BIDS in the near future, but we don’t have a timeline for it yet.