qsiprep.workflows.dwi.distortion_group_merge module

Merging Distortion Groups.

Merging Distortion Groups

qsiprep.workflows.dwi.distortion_group_merge.init_distortion_group_merge_wf(merging_strategy, inputs_list, source_file, output_prefix, name, assembly=None, units=()) → LiterateWorkflow[source]

Combine the finalized DWI series of several correction units into one output.

merging_strategy selects averaging or concatenation.

The inputnode has the following fields for each entry in inputs_list:

[workflow_name]_image...

One input for each volume in each input image.

[workflow_name]_bval...

One input for each input image. path to the corresponding bval file

[workflow_name]_bvec...

One input for each input image. path to the corresponding final bvec file

[workflow_name]_original_bvec...

One input for each input image. Path to the original bvec file

[workflow_name]_original_image...

One input for each input image. Path to the original dwi file

[workflow_name]_raw_concatenated_image

One input for each input image. Path to the original images after concatenation

[workflow_name]_confounds

One input for each input image. Path to the confounds files

[workflow_name]_b0_ref

One input for each input image. Path to the b=0 reference image

[workflow_name]_carpetplot_data

One input for each input image. Path to the hmc carpetplot data

Parameters:

  • merging_strategy (str) – ‘average’: averages images that originally sampled the same q-space coordinate ‘concat’: concatenates images in the 4th dimension

  • inputs_list (list of str) – List if identifiers for inputs. There will be bvals, bvecs, niis and original bvecs.

  • source_file (str) – Source file (relative to the dwi/ directory) used to name the merged derivatives and reports.

  • output_prefix (str) – Prefix for the merged DWI series and the series QC file.

  • name (str) – Name of workflow

  • assembly (OutputAssembly, optional) – The plan assembly this workflow realizes; with units (the member PreprocUnits) it drives the merged output’s provenance sidecar and the gradient plot’s phase-encoding colors.

  • units (tuple of PreprocUnit, optional) – The correction units being merged. Their phase encoding directions color the gradient plot, and they are recorded in the provenance sidecar when assembly is given.

Outputs:

  • merged_image – The input images merged into a single image (averaged or concatenated)

  • merged_bval – The bvals corresponding to merged_image

  • bvecs_t1 – The bvecs corresponding to merged_image, in ACPC space

  • t1_b0_ref – The b=0 reference of the merged series, in ACPC space

  • dwi_mask_t1 – Brain mask for the merged series, in ACPC space

  • cnr_map_t1 – Contrast-to-noise map for the merged series