qsiprep.workflows.fieldmap.syn module

Fieldmap-less estimation (experimental)

In the absence of direct measurements of fieldmap data, we provide an (experimental) option to estimate the susceptibility distortion based on the ANTs symmetric normalization (SyN) technique. This feature may be enabled, using the --use-syn-sdc flag, and will only be applied if fieldmaps are unavailable.

During the evaluation phase, the --force-syn flag will cause this estimation to be performed in addition to fieldmap-based estimation, to permit the direct comparison of the results of each technique. Note that, even if --force-syn is given, the functional outputs of qsiprep will be corrected using the fieldmap-based estimates.

Feedback will be enthusiastically received.

class qsiprep.workflows.fieldmap.syn.ThreshAndBin(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

in_file (a pathlike object or string representing a file) – File to modify, atlas.

Optional Inputs:

atlas_threshold (an integer) – Threshold value.

Outputs:

out_file (a pathlike object or string representing an existing file) – File with threshold and binarization applied.

qsiprep.workflows.fieldmap.syn.init_syn_sdc_wf(bold_pe=None, atlas_threshold=2)

This workflow takes a skull-stripped T1w image and reference b0 image and estimates a susceptibility distortion correction warp, using ANTs symmetric normalization (SyN) and the average fieldmap atlas described in [Treiber2016].

SyN deformation is restricted to the phase-encoding (PE) direction. If no PE direction is specified, anterior-posterior PE is assumed.

SyN deformation is also restricted to regions that are expected to have a >2mm (approximately 1 voxel) warp, based on the fieldmap atlas.

This technique is a variation on those developed in [Huntenburg2014] and [Wang2017].

(Source code)

Inputs

b0_ref

reference image

templatestr

Name of template targeted by template output space

t1_brain

skull-stripped, bias-corrected structural image

t1_2_mni_reverse_transform

inverse registration transform of T1w image to MNI template

Outputs

out_reference

the bold_ref image after unwarping

out_reference_brain

the bold_ref_brain image after unwarping

out_warp

the corresponding DFM compatible with ANTs

out_mask

mask of the unwarped input file