qsiprep.workflows.fieldmap.base module

Automatic selection of the appropriate SDC method

If the dataset metadata indicate that more than one field map acquisition is IntendedFor (see BIDS Specification section 8.9) the following priority will be used:

Table of behavior (fieldmap use-cases):

Fieldmaps found

use_syn

force_syn

Action

True

True

Fieldmaps + SyN

True

False

Fieldmaps

False

True

SyN

False

True

False

SyN

False

False

False

HMC only
qsiprep.workflows.fieldmap.base.init_sdc_wf(fieldmap_info, dwi_meta)[source]

This workflow implements the heuristics to choose a SDC strategy. 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.

(Source code)

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 epi fieldmaps)

  • dwi_meta (dict) – BIDS metadata dictionary corresponding to the DWI run

Inputs:

  • b0_ref – A b0 reference calculated at a previous stage

  • b0_ref_brain – Same as above, but brain-masked

  • b0_mask – Brain mask for the DWI run

  • t1_brain – T1w image, brain-masked, for the fieldmap-less SyN method

  • t1_2_mni_reverse_transform – MNI-to-T1w transform to map prior knowledge to the T1w fo the fieldmap-less SyN method

  • template (str) – Name of template targeted by template output space

Outputs:

  • b0_ref – An unwarped b0 reference

  • b0_mask – The corresponding new mask after unwarping

  • out_warp – The deformation field to unwarp the susceptibility distortions

  • syn_b0_ref – If --force-syn, an unwarped b0 reference with this method (for reporting purposes)

  • method – Name of the method used for SDC

  • fieldmap_hz – The fieldmap in Hz for eddy