SDC workflows coordination.
fieldmap_wrangler(layout, target_image, use_syn=False, force_syn=False)¶
Query the BIDSLayout for fieldmaps, and arrange them for the orchestration workflow.
init_sdc_estimate_wf(fmaps, epi_meta, omp_nthreads=1, debug=False)¶
Build a SDC workflow.
This workflow implements the heuristics to choose an estimation methodology for SDC. When no field map information is present within the BIDS inputs, the EXPERIMENTAL “fieldmap-less SyN” can be performed, using the
--force-synis specified, then the “fieldmap-less SyN” is always executed and reported despite of other fieldmaps available with higher priority. In the latter case (some sort of fieldmap(s) is available and
--force-synis requested), then the SDC method applied is that with the highest priority.
fmaps (list of pybids dicts) – A list of dictionaries with the available fieldmaps (and their metadata using the key
'metadata'for the case of PEPOLAR fieldmaps).
epi_meta (dict) – BIDS metadata dictionary corresponding to the EPI run (i.e., suffix
dwi) for which the fieldmap is being estimated.
omp_nthreads (int) – Maximum number of threads an individual process may use
debug (bool) – Enable debugging outputs
epi_file – A reference image calculated at a previous stage
epi_brain – Same as above, but brain-masked
epi_mask – Brain mask for the run
t1w_brain – T1w image, brain-masked, for the fieldmap-less SyN method
std2anat_xfm – Standard-to-T1w transform generated during spatial normalization (only for the fieldmap-less SyN method).
epi_corrected – The EPI scan reference after unwarping.
epi_mask – The corresponding new mask after unwarping
epi_brain – Brain-extracted, unwarped EPI scan reference
out_warp – The deformation field to unwarp the susceptibility distortions
syn_ref – If
--force-syn, an unwarped EPI scan reference with this method (for reporting purposes)
method (str) – Short description of the estimation method that was run.