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Workflow
Under construction. A description of the workflows.
Workflow modules coordinate the various resource modules to construct the actual pipeline used on MRI data. Currently three workflows exist, one for controlling AFNI resources, one for ASHS, and one for refacing T1w files (for NDA submissions). It is planned to add workflows for FreeSurfer and fMRIprep.
ASHS and reface modules/pipelines are simply a call for their respective resource module, but despite their redundancy are included here for project consistency.
Detailed descriptions are available here, assuming sphinx is cooperative.
Automated segmentation of hippocampal subfields for a single subject is controlled by control_ashs.control_hippseg. While not interacting with EPI data, these masks will likely be used to target HC subfield regions for functional analyses. Requires a singularity image of this container.
This workflow supports defacing, refacing (default), or reface_plus (so special) of T1w files. We currently do not incorporate de/re/plus facing in our pre-processing pipelines, hence the separate workflow, but reface T1w files for NDA hosting.
A number of AFNI-based pipelines are available in this workflow module, both for single-subject as well as group-level analyses and also for both task-based and resting state analyses.
Post fMRIprep AFNI-based pre-processing for task and resting state analyses is controlled by this function.