qsiprep.workflows.dwi.registration module

qsiprep.workflows.dwi.registration.init_b0_to_anat_registration_wf(write_report=True, transform_type='Rigid', name='b0_anat_coreg')[source]

Calculates the registration between a reference b0 image and T1-space using antsRegistration

../_images/qsiprep-workflows-dwi-registration-1.png

(Source code, png, svg, pdf)

Parameters:

  • mem_gb (float) – Size of DWI file in GB

  • omp_nthreads (int) – Maximum number of threads an individual process may use

  • name (str) – Name of workflow (default: bold_reg_wf)

  • transform_type (str) – Either “Rigid” or “Affine”

  • write_report (bool) – Should a reportlet be written?

Inputs:

  • ref_b0_brain – Reference image to which DWI series is aligned If fieldwarp == True, ref_bold_brain should be unwarped

  • t1_brain – Skull-stripped t1_preproc

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

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • subject_id – FreeSurfer subject ID

Outputs:

  • itk_b0_to_t1 – Affine transform from ref_bold_brain to T1 space (ITK format)

  • itk_t1_to_b0 – Affine transform from T1 space to DWI space (ITK format)

  • coreg_metric – Mattes score from the coregistration

  • fallback – Boolean indicating whether BBR was rejected (mri_coreg registration returned)

  • report – svg reportlet for the coregistration

qsiprep.workflows.dwi.registration.init_direct_b0_acpc_wf(write_report=True, name='b0_anat_coreg')[source]

Re-orients a b=0 image directly to AC-PC. A full affine registration is run, but only the rigid (translation + rotation) part is included.

(Source code)

Parameters
baby_modebool

Use the infant t1w brain as the reference volume

mem_gbfloat

Size of DWI file in GB

omp_nthreadsint

Maximum number of threads an individual process may use

namestr

Name of workflow (default: bold_reg_wf)

transform_typestr

Either “Rigid” or “Affine”

write_reportbool

Should a reportlet be written?

Inputs

ref_b0_brain

Reference image to which DWI series is aligned If fieldwarp == True, ref_bold_brain should be unwarped

t1_brain

Standard space brain, either adult or infant template

t1_seg

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

subjects_dir

FreeSurfer SUBJECTS_DIR

subject_id

FreeSurfer subject ID

Outputs

itk_b0_to_t1

Affine transform from ref_bold_brain to T1 space (ITK format)

itk_t1_to_b0

Affine transform from T1 space to DWI space (ITK format)

coreg_metric

Mattes score from the coregistration

report

svg reportlet for the coregistration