dmriprep.workflows.dwi package

Submodules

dmriprep.workflows.dwi.artifacts module

Artefact removal and resizing

dmriprep.workflows.dwi.artifacts.init_dwi_artifacts_wf(ignore, output_resolution)[source]

This workflow performs denoising and unringing on the input dwi image.

_images/dmriprep-workflows-dwi-1.png

(Source code, png, svg, pdf)

Parameters

ignorelist

List of artefact removal steps to skip (default: [])

Inputs

dwi_filestr

dwi NIfTI file

Outputs

out_filestr

dwi NIfTI file after artefact removal

dmriprep.workflows.dwi.artifacts.init_dwi_artifacts_wf(ignore, output_resolution)[source]

This workflow performs denoising and unringing on the input dwi image.

_images/dmriprep-workflows-dwi-2.png

(Source code, png, svg, pdf)

Parameters

ignorelist

List of artefact removal steps to skip (default: [])

Inputs

dwi_filestr

dwi NIfTI file

Outputs

out_filestr

dwi NIfTI file after artefact removal

dmriprep.workflows.dwi.base module

Orchestrating the dwi preprocessing workflows

dmriprep.workflows.dwi.base.init_dwi_preproc_wf(layout, output_dir, subject_id, dwi_file, b0_thresh, output_resolution, bet_dwi, bet_mag, acqp_file, slspec_file, omp_nthreads, ignore, use_ants, use_brainsuite, synb0_dir)[source]

This workflow controls the diffusion preprocessing stages of dMRIprep.

(Source code)

dmriprep.workflows.dwi.base.init_dwi_preproc_wf(layout, output_dir, subject_id, dwi_file, b0_thresh, output_resolution, bet_dwi, bet_mag, acqp_file, slspec_file, omp_nthreads, ignore, use_ants, use_brainsuite, synb0_dir)[source]

This workflow controls the diffusion preprocessing stages of dMRIprep.

(Source code)

dmriprep.workflows.dwi.eddy module

Head motion, eddy current distortion and EPI distortion correction

dmriprep.workflows.dwi.eddy.init_dwi_eddy_wf(omp_nthreads, sdc_method=None, name='dwi_eddy_wf')[source]

This workflow runs eddy on the input dwi image.

_images/dmriprep-workflows-dwi-5.png

(Source code, png, svg, pdf)

Parameters

omp_nthreads: int

Number of threads to run eddy

sdc_method: str

Synthetic distortion correction method (may include ‘fieldmap or ‘topup’)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

fieldmap_file

fieldmap file

topup_fieldcoef

topup file containing field coefficients

topup_movpar

topup movpar.txt file

acqp

acquisition parameters file

index

index file

slspec

slspec file

Outputs

out_file

output eddy-corrected dwi image

out_bvec

output rotated bvecs after eddy correction

dmriprep.workflows.dwi.eddy.init_dwi_eddy_wf(omp_nthreads, sdc_method=None, name='dwi_eddy_wf')[source]

This workflow runs eddy on the input dwi image.

_images/dmriprep-workflows-dwi-6.png

(Source code, png, svg, pdf)

Parameters

omp_nthreads: int

Number of threads to run eddy

sdc_method: str

Synthetic distortion correction method (may include ‘fieldmap or ‘topup’)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

fieldmap_file

fieldmap file

topup_fieldcoef

topup file containing field coefficients

topup_movpar

topup movpar.txt file

acqp

acquisition parameters file

index

index file

slspec

slspec file

Outputs

out_file

output eddy-corrected dwi image

out_bvec

output rotated bvecs after eddy correction

dmriprep.workflows.dwi.outputs module

Output dwi

dmriprep.workflows.dwi.outputs.init_dwi_derivatives_wf(subject_id, session_id, output_folder)[source]
dmriprep.workflows.dwi.outputs.init_dwi_derivatives_wf(subject_id, session_id, output_folder)[source]

dmriprep.workflows.dwi.qc module

dmriprep.workflows.dwi.qc.createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file)[source]
dmriprep.workflows.dwi.qc.createSprite4D(dwi_file)[source]
dmriprep.workflows.dwi.qc.create_report_json(dwi_corrected_file, eddy_rms, eddy_report, color_fa_file, anat_mask_file, outlier_indices, eddy_qc_file, outpath='/home/docs/checkouts/readthedocs.org/user_builds/dmriprep-personal/checkouts/refactor/docs/report.json')[source]
dmriprep.workflows.dwi.qc.create_sprite_from_tiles(tile, out_file=None, as_bytes=False)[source]
dmriprep.workflows.dwi.qc.get_middle_slices(data, slice_direction)[source]
dmriprep.workflows.dwi.qc.load_and_reorient(filename)[source]
dmriprep.workflows.dwi.qc.mplfig(data, outfile=None, as_bytes=False)[source]
dmriprep.workflows.dwi.qc.mplfigcontour(data, outfile=None, as_bytes=False)[source]
dmriprep.workflows.dwi.qc.nearest_square(limit)[source]
dmriprep.workflows.dwi.qc.reorient_array(data, aff)[source]
dmriprep.workflows.dwi.qc.reshape3D(data, n=256)[source]
dmriprep.workflows.dwi.qc.reshape4D(data, n=256)[source]

dmriprep.workflows.dwi.tensor module

Tensor fitting

dmriprep.workflows.dwi.tensor.init_dwi_tensor_wf()[source]

This workflow fits a tensor to the input dwi image.

_images/dmriprep-workflows-dwi-7.png

(Source code, png, svg, pdf)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

Outputs

FA_file

FA

MD_file

MD

AD_file

AD

RD_file

RD

V1_file

V1

sse_file

diffusion tensor fit residuals

dmriprep.workflows.dwi.tensor.init_dwi_tensor_wf()[source]

This workflow fits a tensor to the input dwi image.

_images/dmriprep-workflows-dwi-8.png

(Source code, png, svg, pdf)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

Outputs

FA_file

FA

MD_file

MD

AD_file

AD

RD_file

RD

V1_file

V1

sse_file

diffusion tensor fit residuals

dmriprep.workflows.dwi.util module

Utility workflows

dmriprep.workflows.dwi.util.init_dwi_concat_wf(layout, ref_file, dwi_list)[source]

This workflow concatenates a list of dwi images as well as their associated bvecs and bvals.

(Source code)

Parameters

layoutstr

reference dwi NIfTI file for naming outputs

Inputs

ref_file

reference dwi NIfTI file

dwi_listlist

list of dwi NIfTI files

Outputs

dwi_filestr

concatenated dwi NIfTI file

bvec_file

concatenated bvec file

bval_file

concatenated bval file

dmriprep.workflows.dwi.util.init_dwi_concat_wf(layout, ref_file, dwi_list)[source]

This workflow concatenates a list of dwi images as well as their associated bvecs and bvals.

(Source code)

Parameters

layoutstr

reference dwi NIfTI file for naming outputs

Inputs

ref_file

reference dwi NIfTI file

dwi_listlist

list of dwi NIfTI files

Outputs

dwi_filestr

concatenated dwi NIfTI file

bvec_file

concatenated bvec file

bval_file

concatenated bval file

Module contents

Pre-processing dMRI workflows

Orchestrating the dwi preprocessing workflows

dmriprep.workflows.dwi.base.init_dwi_preproc_wf(layout, output_dir, subject_id, dwi_file, b0_thresh, output_resolution, bet_dwi, bet_mag, acqp_file, slspec_file, omp_nthreads, ignore, use_ants, use_brainsuite, synb0_dir)[source]

This workflow controls the diffusion preprocessing stages of dMRIprep.

(Source code)

Utility workflows

dmriprep.workflows.dwi.util.init_dwi_concat_wf(layout, ref_file, dwi_list)[source]

This workflow concatenates a list of dwi images as well as their associated bvecs and bvals.

(Source code)

Parameters

layoutstr

reference dwi NIfTI file for naming outputs

Inputs

ref_file

reference dwi NIfTI file

dwi_listlist

list of dwi NIfTI files

Outputs

dwi_filestr

concatenated dwi NIfTI file

bvec_file

concatenated bvec file

bval_file

concatenated bval file

Artefact removal and resizing

dmriprep.workflows.dwi.artifacts.init_dwi_artifacts_wf(ignore, output_resolution)[source]

This workflow performs denoising and unringing on the input dwi image.

_images/dmriprep-workflows-dwi-13.png

(Source code, png, svg, pdf)

Parameters

ignorelist

List of artefact removal steps to skip (default: [])

Inputs

dwi_filestr

dwi NIfTI file

Outputs

out_filestr

dwi NIfTI file after artefact removal

Head motion, eddy current distortion and EPI distortion correction

dmriprep.workflows.dwi.eddy.init_dwi_eddy_wf(omp_nthreads, sdc_method=None, name='dwi_eddy_wf')[source]

This workflow runs eddy on the input dwi image.

_images/dmriprep-workflows-dwi-14.png

(Source code, png, svg, pdf)

Parameters

omp_nthreads: int

Number of threads to run eddy

sdc_method: str

Synthetic distortion correction method (may include ‘fieldmap or ‘topup’)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

fieldmap_file

fieldmap file

topup_fieldcoef

topup file containing field coefficients

topup_movpar

topup movpar.txt file

acqp

acquisition parameters file

index

index file

slspec

slspec file

Outputs

out_file

output eddy-corrected dwi image

out_bvec

output rotated bvecs after eddy correction

Tensor fitting

dmriprep.workflows.dwi.tensor.init_dwi_tensor_wf()[source]

This workflow fits a tensor to the input dwi image.

_images/dmriprep-workflows-dwi-15.png

(Source code, png, svg, pdf)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

Outputs

FA_file

FA

MD_file

MD

AD_file

AD

RD_file

RD

V1_file

V1

sse_file

diffusion tensor fit residuals

Output dwi

dmriprep.workflows.dwi.outputs.init_dwi_derivatives_wf(subject_id, session_id, output_folder)[source]
dmriprep.workflows.dwi.init_dwi_preproc_wf(layout, output_dir, subject_id, dwi_file, b0_thresh, output_resolution, bet_dwi, bet_mag, acqp_file, slspec_file, omp_nthreads, ignore, use_ants, use_brainsuite, synb0_dir)[source]

This workflow controls the diffusion preprocessing stages of dMRIprep.

(Source code)

dmriprep.workflows.dwi.init_dwi_concat_wf(layout, ref_file, dwi_list)[source]

This workflow concatenates a list of dwi images as well as their associated bvecs and bvals.

(Source code)

Parameters

layoutstr

reference dwi NIfTI file for naming outputs

Inputs

ref_file

reference dwi NIfTI file

dwi_listlist

list of dwi NIfTI files

Outputs

dwi_filestr

concatenated dwi NIfTI file

bvec_file

concatenated bvec file

bval_file

concatenated bval file

dmriprep.workflows.dwi.init_dwi_artifacts_wf(ignore, output_resolution)[source]

This workflow performs denoising and unringing on the input dwi image.

_images/dmriprep-workflows-dwi-18.png

(Source code, png, svg, pdf)

Parameters

ignorelist

List of artefact removal steps to skip (default: [])

Inputs

dwi_filestr

dwi NIfTI file

Outputs

out_filestr

dwi NIfTI file after artefact removal

dmriprep.workflows.dwi.init_dwi_eddy_wf(omp_nthreads, sdc_method=None, name='dwi_eddy_wf')[source]

This workflow runs eddy on the input dwi image.

_images/dmriprep-workflows-dwi-19.png

(Source code, png, svg, pdf)

Parameters

omp_nthreads: int

Number of threads to run eddy

sdc_method: str

Synthetic distortion correction method (may include ‘fieldmap or ‘topup’)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

fieldmap_file

fieldmap file

topup_fieldcoef

topup file containing field coefficients

topup_movpar

topup movpar.txt file

acqp

acquisition parameters file

index

index file

slspec

slspec file

Outputs

out_file

output eddy-corrected dwi image

out_bvec

output rotated bvecs after eddy correction

dmriprep.workflows.dwi.init_dwi_tensor_wf()[source]

This workflow fits a tensor to the input dwi image.

_images/dmriprep-workflows-dwi-20.png

(Source code, png, svg, pdf)

Inputs

dwi_file

dwi NIfTI file

bvec_file

bvec file

bval_file

bval file

mask_file

brain mask file

Outputs

FA_file

FA

MD_file

MD

AD_file

AD

RD_file

RD

V1_file

V1

sse_file

diffusion tensor fit residuals

dmriprep.workflows.dwi.init_dwi_derivatives_wf(subject_id, session_id, output_folder)[source]