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.

  • SCATTR 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. SCATTR makes use of pybids to parse the dataset, so we suggest using the BIDS Validator to ensure your dataset has no errors.

If you passed Freesurfer or diffusion derivative locations (--freesurfer-dir or --dwi-dir), you may get get this message as the files are a different location than in the input directory provided.

2. What if I want to use merge two different atlases?

SCATTR uses labelmerge to combine labels from different atlases. To that end, we have exposed the labelmerge command-line arguments, enabling substitution of different atlases. These arguments are pre-pended with --labelmerge_<labelmerge_arg>. We encourage you to check out the labelmerge documention (linked above), as well as SCATTR’s help command to see all available options.

NOTE: If using a different atlas, you will need to ensure that the associated metadata is available (according to the BIDS specification) for each subject part of the input dataset and in the same space as the T1w image.

3. I only want to use labels from a single atlas.

If you only want to use a labels from a single atlas (e.g. skip labelmerge), you can invoke the --skip_labelmerge argument. If you are using this flag, you can combine this with the --labelmerge_base_dir and --labelmerge_base_desc arguments to provide your own atlas. Similar to using custom atlases (from 2), it is expected that the imaging and associated metadata is available for all subjects in the dataset and that all files follow the BIDS specification.