qsiprep.workflows.dwi.pre_hmc module
Orchestrating the dwi-preprocessing workflow
- qsiprep.workflows.dwi.pre_hmc.init_dwi_pre_hmc_wf(scan_groups, preprocess_rpe_series, orientation, source_file, calculate_qc=True, name='pre_hmc_wf')[source]
This workflow merges and denoises dwi scans. The outputs from this workflow is a single dwi file (optionally denoised) 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
preprocess_rpe_seriesisTrue. FSL’s eddy also requires data in LAS+ orientation.Parameters
- orientationstr
‘LPS’ or ‘LAS’
- 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)