Warning: This document is for an old version of sdcflows. The main version is master.

sdcflows.workflows.base module

SDC workflows coordination.

sdcflows.workflows.base.fieldmap_wrangler(layout, target_image, use_syn=False, force_syn=False)[source]

Query the BIDSLayout for fieldmaps, and arrange them for the orchestration workflow.

sdcflows.workflows.base.init_sdc_estimate_wf(fmaps, epi_meta, omp_nthreads=1, debug=False)[source]

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 --use-syn argument. When --force-syn is 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-syn is requested), then the SDC method applied is that with the highest priority.

Parameters
  • 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 bold, sbref, or 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

Inputs
  • 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).

Outputs
  • 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.