How to re-run a few failed subjects/add new subjects to an old RABIES run

The --inherit_unbiased_template preprocessing parameter was designed for cases where a subset of scans failed registration, or new scans need to be added to a study, without re-running the pipeline for all previously well-registered scans. Specifically, this parameter allows to recycle the unbiased study template generated by an old RABIES run, and register each scan directly to this template and instead of re-generating a new one from the input data (which would require re-running the commonspace registration across the entire dataset).

To use this parameter, you can point --inherit_unbiased_template to the path of a previously completed RABIES run, and combine this with --inclusion_ids to only preprocess a selected set of scans within the BIDs directory (if it is shared with the rest of the study dataset):

rabies --inclusion_ids /full_path/bids_inputs/.../selected_scan1.nii.gz /full_path/bids_inputs/.../selected_scan2.nii.gz \
preprocess bids_inputs/ preprocess_outputs_selected_scans_only/ \
--inherit_unbiased_template /path_to_my_old_RABIES_preprocess_output

Importantly, you will note that you must provide some new output directory for this independent RABIES run, and it is considered independent for downstream RABIES stages, as there is currently no way to fully merge together two different RABIES runs.

Also note that by selecting this option, the following preprocessing parameters will be overriden to enforce consistency with the previous run: --anatomical_resampling, --commonspace_reg, --anat_template, --brain_mask, --WM_mask, --CSF_mask, --vascular_mask.