qsiprep.workflows.dwi.pre_hmc module

Orchestrating the dwi-preprocessing workflow.

Orchestrating the dwi-preprocessing workflow

qsiprep.workflows.dwi.pre_hmc.init_dwi_pre_hmc_wf(unit, orientation, source_file, do_biascorr, calculate_qc=True, name='pre_hmc_wf')[source]

Build a workflow that merges denoised dwi scans before head motion correction.

The member series arrive already conformed and denoised (see init_dwi_series_denoise_wf()), one list entry per file in unit.dwi_files and in the same order. The outputs from this workflow are a single dwi file and corresponding bvals, bvecs.

In the general case, a single warped group will be sent to this workflow. However, since eddy expects a single 4D input file, two warped groups can be processed separately and merged into a 4D file. This happens when the unit has both phase encoding polarities (unit.has_bidirectional_dwi). FSL’s eddy also requires data in LAS+ orientation.

../_images/qsiprep-workflows-dwi-pre_hmc-1.png

(Source code, png, svg, pdf)

Parameters:

  • unit (PreprocUnit) – The DWI series to merge. When the unit has both phase encoding polarities, each polarity is merged separately.

  • orientation (str) – ‘LPS’ or ‘LAS’, the orientation the series were conformed to

  • source_file (str) – Source file used to name the merged outputs when the unit has a single phase encoding polarity.

  • do_biascorr (bool) – Whether bias correction is applied to this output; used to write the methods boilerplate.

  • calculate_qc (bool, optional) – Whether to calculate model-free QC metrics for the merged series when the unit has a single phase encoding polarity. Default is True.

  • name (str, optional) – Name of workflow (default: pre_hmc_wf)

Inputs:

  • dwi_files – conformed, denoised series, one per file in unit.dwi_files

  • bval_files – bvals of each series

  • bvec_files – conformed bvecs of each series

  • raw_dwi_files – conformed, not denoised series

  • noise_images – noise image of each series

  • denoising_confounds – denoising confounds of each series

  • validation_reports – conformation report of each series

Outputs:

  • dwi_file – a (potentially-denoised) dwi file

  • bvec_file – a bvec file

  • bval_file – a bval files

  • sidecar_file – a json sidecar file for the scan data

  • b0_indices – list of the positions of the b0 images in the dwi series

  • b0_images – list of paths to single-volume b0 images

  • original_files – list of paths to the original files that the single volumes came from

  • original_grouping – list of warped space group ids

  • raw_concatenated – 4d image of the raw inputs concatenated (for QC and visualization)