qsiprep.workflows.dwi.resampling module

Resampling workflows

qsiprep.workflows.dwi.resampling.init_dwi_trans_wf(source_file, mem_gb, template='ACPC', name='dwi_trans_wf', use_compression=True, write_local_bvecs=False, write_reports=True, concatenate=True, doing_topup=False)

This workflow samples dwi images to the output_grid in a “single shot” from the original DWI series.

(Source code)

Parameters

templatestr

Name of template targeted by template output space

mem_gbfloat

Size of DWI file in GB

omp_nthreadsint

Maximum number of threads an individual process may use

namestr

Name of workflow (default: dwi_trans_wf)

use_compressionbool

Save registered DWI series as .nii.gz

use_fieldwarpbool

Include SDC warp in single-shot transform from DWI to MNI

output_resolutionfloat

Voxel size in mm for the output data

to_mnibool

Include warps to MNI

write_local_bvecsbool

if true, local bvec niftis are written

Inputs

itk_b0_to_t1

Affine transform from ref_bold_brain to T1 space (ITK format)

t1_2_mni_forward_transform

ANTs-compatible affine-and-warp transform file

dwi_files

Individual 3D volumes, not motion corrected

cnr_map

Contrast to noise map from model-based hmc

fieldmap_hz

Fieldmap in Hz. Only written out if TOPUP was used.

bval_files

individual bval files

bvec_files

one-lined bvec files

b0_ref_image

b0 template for the dwi series

b0_indices

List of indices that contain a b0 image

dwi_mask

Skull-stripping mask of reference image

name_source

DWI series NIfTI file Used to recover original information lost during processing

hmc_xforms

List of affine transforms aligning each volume to ref_image in ITK format

fieldwarps

a DFM in ITK format

output_grid

File defining the output space

t1_mask

Brain mask from the t1w

Outputs

dwi_resampled

DWI series, resampled to template space. One file if concatenate, otherwise a list of files

dwi_ref_resampled

Reference, contrast-enhanced summary of the DWI series, resampled to template space

dwi_mask_resampled

DWI series mask in template space

cnr_map_resampled

Contrast to noise map resampled

bvals

bvals file for the DWI series

rotated_bvecs

bvecs rotated for transforms to output_grid

local_bvecs

NIfTI file containing the bvec rotation matrix (due to transforms) in each voxel. Includes rotations introduced by warpingdenoisin

qsiprep.workflows.dwi.resampling.init_dwi_trans_wf(source_file, mem_gb, template='ACPC', name='dwi_trans_wf', use_compression=True, write_local_bvecs=False, write_reports=True, concatenate=True, doing_topup=False)

This workflow samples dwi images to the output_grid in a “single shot” from the original DWI series.

(Source code)

Parameters

templatestr

Name of template targeted by template output space

mem_gbfloat

Size of DWI file in GB

omp_nthreadsint

Maximum number of threads an individual process may use

namestr

Name of workflow (default: dwi_trans_wf)

use_compressionbool

Save registered DWI series as .nii.gz

use_fieldwarpbool

Include SDC warp in single-shot transform from DWI to MNI

output_resolutionfloat

Voxel size in mm for the output data

to_mnibool

Include warps to MNI

write_local_bvecsbool

if true, local bvec niftis are written

Inputs

itk_b0_to_t1

Affine transform from ref_bold_brain to T1 space (ITK format)

t1_2_mni_forward_transform

ANTs-compatible affine-and-warp transform file

dwi_files

Individual 3D volumes, not motion corrected

cnr_map

Contrast to noise map from model-based hmc

fieldmap_hz

Fieldmap in Hz. Only written out if TOPUP was used.

bval_files

individual bval files

bvec_files

one-lined bvec files

b0_ref_image

b0 template for the dwi series

b0_indices

List of indices that contain a b0 image

dwi_mask

Skull-stripping mask of reference image

name_source

DWI series NIfTI file Used to recover original information lost during processing

hmc_xforms

List of affine transforms aligning each volume to ref_image in ITK format

fieldwarps

a DFM in ITK format

output_grid

File defining the output space

t1_mask

Brain mask from the t1w

Outputs

dwi_resampled

DWI series, resampled to template space. One file if concatenate, otherwise a list of files

dwi_ref_resampled

Reference, contrast-enhanced summary of the DWI series, resampled to template space

dwi_mask_resampled

DWI series mask in template space

cnr_map_resampled

Contrast to noise map resampled

bvals

bvals file for the DWI series

rotated_bvecs

bvecs rotated for transforms to output_grid

local_bvecs

NIfTI file containing the bvec rotation matrix (due to transforms) in each voxel. Includes rotations introduced by warpingdenoisin