Frequently Asked Questions (FAQs)

1. Why do I get the error No input images found for <modality>?

The workflow was unable to find the required input files from the input BIDS directory. This can happen if:

• Singularity or Docker cannot access your input directory. For Singularity, ensure your Singularity options are appropriate, in particular SINGULARITY_BINDPATH. For Docker, ensure you are mounting the correct directory with the -v flag described in the Getting Started section.

• Labelmerge does not recognize your BIDS-formatted input images. This can occur if, for example, T1w images are labelled with the suffix t1w.nii.gz instead of T1w.nii.gz as per BIDS specifications. Labelmerge makes use of pybids to parse the dataset, so we suggest using the BIDS Validator to ensure your dataset has no errors.