Identifying field-mapping resources

Base fieldmap estimation

• Subject can have phase-difference data.
• Subject can have a fieldmap acquisition.

fmriprep.workflows.fieldmap.base.init_fmap_estimator_wf(fmap_bids, reportlets_dir, omp_nthreads, fmap_bspline)

This workflow selects the fieldmap estimation data available for the subject and returns the estimated fieldmap in mm, along with a corresponding reference image. Current implementation applies the first type of fieldmap estimation found in the following order of precedence:

• “Natural” fieldmaps
• Phase-difference fieldmaps

Outputs:

fmap

The estimated fieldmap itself IN UNITS OF Hz.

fmap_ref

the anatomical reference for the fieldmap (magnitude image, corrected SEm, etc.)

fmap_mask

a brain mask for the fieldmap

fmriprep.workflows.fieldmap.base.init_fmap_unwarp_report_wf(reportlets_dir, name='fmap_unwarp_report_wf')

This workflow generates and saves a reportlet showing the effect of fieldmap unwarping a BOLD image.

(Source code, png, svg, pdf)

Parameters

reportlets_dir : str

Directory in which to save reportlets

name : str, optional

Workflow name (default: fmap_unwarp_report_wf)

Inputs

in_pre

Reference image, before unwarping

in_post

Reference image, after unwarping

in_seg

Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

in_xfm

Affine transform from T1 space to BOLD space (ITK format)

name_source

BOLD series NIfTI file Used to recover original information lost during processing