qsiprep.workflows.dwi.base module

Orchestrating the dwi-preprocessing workflow

qsiprep.workflows.dwi.base.init_dwi_preproc_wf(scan_groups, t2w_sdc, output_prefix, source_file, anatomical_template) → LiterateWorkflow[source]

This workflow controls the dwi preprocessing stages of qsiprep.

(Source code)

Parameters:

  • scan_groups (list of dicts) – List of dicts grouping files by PE-dir

  • t2w_sdc (bool) – Include T2w scans in distortion correction

  • output_prefix (str) – beginning of the output file name (eg ‘sub-1_buds-j’)

  • source_file (str) – The file name template used for derivatives

Inputs:

  • t1_preproc – Bias-corrected structural template image

  • t1_brain – Skull-stripped t1_preproc

  • t1_mask – Mask of the skull-stripped template image

  • t1_output_grid – Image to write out DWIs aligned to t1

  • t1_seg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

  • t1_2_mni_forward_transform – ANTs-compatible affine-and-warp transform file

  • t1_2_mni_reverse_transform – ANTs-compatible affine-and-warp transform file (inverse)

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • subject_id – FreeSurfer subject ID

  • dwi_sampling_grid – A NIfTI1 file with the grid spacing and FoV to resample the DWIs

Outputs:

  • dwi_t1 – dwi series, resampled to T1w space

  • dwi_mask_t1 – dwi series mask in T1w space

  • bvals_t1 – bvalues of the dwi series

  • bvecs_t1 – bvecs after aligning to the T1w and resampling

  • local_bvecs_t1 – voxelwise bvecs accounting for local displacements

  • gradient_table_t1 – MRTrix-style gradient table

  • dwi_mni – dwi series, resampled to template space

  • dwi_mask_mni – dwi series mask in template space

  • bvals_mni – bvalues of the dwi series

  • bvecs_mni – bvecs after aligning to the T1w and resampling

  • local_bvecs_mni – voxelwise bvecs accounting for local displacements

  • gradient_table_mni – MRTrix-style gradient table

  • confounds_file – estimated motion parameters and zipper scores

  • raw_qc_file – DSI Studio QC file for the raw data

  • raw_concatenated – concatenated raw images for a qc report

  • carpetplot_data – path to a file containing carpetplot data

See also

qsiprep.workflows.dwi.base.init_dwi_preproc_wf(scan_groups, t2w_sdc, output_prefix, source_file, anatomical_template) → LiterateWorkflow[source]

This workflow controls the dwi preprocessing stages of qsiprep.

(Source code)

Parameters:

  • scan_groups (list of dicts) – List of dicts grouping files by PE-dir

  • t2w_sdc (bool) – Include T2w scans in distortion correction

  • output_prefix (str) – beginning of the output file name (eg ‘sub-1_buds-j’)

  • source_file (str) – The file name template used for derivatives

Inputs:

  • t1_preproc – Bias-corrected structural template image

  • t1_brain – Skull-stripped t1_preproc

  • t1_mask – Mask of the skull-stripped template image

  • t1_output_grid – Image to write out DWIs aligned to t1

  • t1_seg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

  • t1_2_mni_forward_transform – ANTs-compatible affine-and-warp transform file

  • t1_2_mni_reverse_transform – ANTs-compatible affine-and-warp transform file (inverse)

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • subject_id – FreeSurfer subject ID

  • dwi_sampling_grid – A NIfTI1 file with the grid spacing and FoV to resample the DWIs

Outputs:

  • dwi_t1 – dwi series, resampled to T1w space

  • dwi_mask_t1 – dwi series mask in T1w space

  • bvals_t1 – bvalues of the dwi series

  • bvecs_t1 – bvecs after aligning to the T1w and resampling

  • local_bvecs_t1 – voxelwise bvecs accounting for local displacements

  • gradient_table_t1 – MRTrix-style gradient table

  • dwi_mni – dwi series, resampled to template space

  • dwi_mask_mni – dwi series mask in template space

  • bvals_mni – bvalues of the dwi series

  • bvecs_mni – bvecs after aligning to the T1w and resampling

  • local_bvecs_mni – voxelwise bvecs accounting for local displacements

  • gradient_table_mni – MRTrix-style gradient table

  • confounds_file – estimated motion parameters and zipper scores

  • raw_qc_file – DSI Studio QC file for the raw data

  • raw_concatenated – concatenated raw images for a qc report

  • carpetplot_data – path to a file containing carpetplot data

See also