qsiprep.workflows.dwi.finalize module

Final steps on the preprocessed data

qsiprep.workflows.dwi.finalize.init_dwi_finalize_wf(scan_groups, name, source_file, output_prefix, write_derivatives=True)

This workflow controls the resampling parts of the dwi preprocessing workflow.

(Source code)

Parameters

output_prefixstr

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

ignorelist

Preprocessing steps to skip (eg “fieldmaps”)

templatestr

Name of template targeted by template output space

output_dirstr

Directory in which to save derivatives

output_resolutionfloat

Output voxel resolution in mm

pepolar_methodstr

Either ‘DRBUDDI’, ‘TOPUP’ or ‘TOPUP+DRBUDDI’. The method for SDC when EPI fieldmaps are used.

omp_nthreadsint

Maximum number of threads an individual process may use

low_membool

Write uncompressed .nii files in some cases to reduce memory usage

layoutBIDSLayout

BIDSLayout structure to enable metadata retrieval

write_derivatives: bool

Is this the final output? If so, write the final derivatives. If these resampled outputs will be combined with other distortion groups at the end, then return the resampled, non-concatenated images

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

b0_ref_image

A Nifti of the b0 reference that was used for hmc and sdc

intramodal_template

The intramodal template image created from all b0 ref images

source_file

The file name template used for derivatives

raw_qc_file

The QC file from the DWI data before any preprocessing

raw_concatenated

The original raw images in a single 4D file

carpetplot_data

File containing carpetplot data

Outputs

dwi_t1

dwi series, resampled to T1w space. If write_derivitaves, this is a 4d file. Otherwise it’s a list of resampled images.

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

qsiprep.workflows.dwi.finalize.init_dwi_finalize_wf(scan_groups, name, source_file, output_prefix, write_derivatives=True)

This workflow controls the resampling parts of the dwi preprocessing workflow.

(Source code)

Parameters

output_prefixstr

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

ignorelist

Preprocessing steps to skip (eg “fieldmaps”)

templatestr

Name of template targeted by template output space

output_dirstr

Directory in which to save derivatives

output_resolutionfloat

Output voxel resolution in mm

pepolar_methodstr

Either ‘DRBUDDI’, ‘TOPUP’ or ‘TOPUP+DRBUDDI’. The method for SDC when EPI fieldmaps are used.

omp_nthreadsint

Maximum number of threads an individual process may use

low_membool

Write uncompressed .nii files in some cases to reduce memory usage

layoutBIDSLayout

BIDSLayout structure to enable metadata retrieval

write_derivatives: bool

Is this the final output? If so, write the final derivatives. If these resampled outputs will be combined with other distortion groups at the end, then return the resampled, non-concatenated images

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

b0_ref_image

A Nifti of the b0 reference that was used for hmc and sdc

intramodal_template

The intramodal template image created from all b0 ref images

source_file

The file name template used for derivatives

raw_qc_file

The QC file from the DWI data before any preprocessing

raw_concatenated

The original raw images in a single 4D file

carpetplot_data

File containing carpetplot data

Outputs

dwi_t1

dwi series, resampled to T1w space. If write_derivitaves, this is a 4d file. Otherwise it’s a list of resampled images.

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

qsiprep.workflows.dwi.finalize.init_finalize_denoising_wf(source_file, do_biascorr, num_dwi_acquisitions, split_biascorr=False, do_patch2self=False, name='final_denoise_wf')

Some denoising can only happen after images have been aligned