aslprep.workflows.asl.registration module

Workflows for registering ASL data.

init_asl_reg_wf(use_bbr, asl2t1w_dof, asl2t1w_init, name='asl_reg_wf', sloppy=False, write_report=True)[source]

Build a workflow to run same-subject, ASL-to-T1w image-registration.

Calculates the registration between a reference ASL image and T1w-space using a boundary-based registration (BBR) cost function.

Workflow Graph
../_images/aslprep-workflows-asl-registration-1.png

(Source code, png, svg, pdf)

Parameters:

  • use_bbr (bool or None) – Enable/disable boundary-based registration refinement. If None, test BBR result for distortion before accepting.

  • asl2t1w_dof (6, 9 or 12) – Degrees-of-freedom for ASL-T1w registration

  • asl2t1w_init (str, ‘header’ or ‘register’) – If 'header', use header information for initialization of ASL and T1 images. If 'register', align volumes by their centers.

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

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

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

  • use_compression (bool) – Save registered ASL series as .nii.gz

  • use_fieldwarp (bool) – Include SDC warp in single-shot transform from ASL to T1

  • write_report (bool) – Whether a reportlet should be stored

Inputs:

  • ref_asl_brain – Reference image to which ASL series is aligned If fieldwarp == True, ref_asl_brain should be unwarped

  • t1w_brain – Skull-stripped t1w_preproc

  • t1w_dseg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

Outputs:

  • itk_asl_to_t1 – Affine transform from ref_asl_brain to T1 space (ITK format)

  • itk_t1_to_asl – Affine transform from T1 space to ASL space (ITK format)

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

init_asl_t1_trans_wf(mem_gb, omp_nthreads, scorescrub=False, basil=False, cbft1space=False, multiecho=False, use_fieldwarp=False, use_compression=True, name='asl_t1_trans_wf')[source]

Co-register the reference ASL image to T1w-space.

The workflow uses BBR.

Workflow Graph
../_images/aslprep-workflows-asl-registration-2.png

(Source code, png, svg, pdf)

Parameters:

  • use_fieldwarp (bool) – Include SDC warp in single-shot transform from ASLto T1

  • multiecho (bool) – If multiecho data was supplied, HMC already performed

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

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

  • use_compression (bool) – Save registered ASL series as .nii.gz

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

Inputs:

  • name_source – ASL series NIfTI file Used to recover original information lost during processing

  • ref_asl_brain – Reference image to which ASL series is aligned If fieldwarp == True, ref_asl_brain should be unwarped

  • ref_asl_mask – Skull-stripping mask of reference image

  • t1w_brain – Skull-stripped bias-corrected structural template image

  • t1w_mask – Mask of the skull-stripped template image

  • asl_split – Individual 3D ASL volumes, not motion corrected

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

  • itk_asl_to_t1 – Affine transform from ref_asl_brain to T1 space (ITK format)

  • fieldwarp – a DFM in ITK format

Outputs:

  • ASL_t1 – Motion-corrected ASL series in T1 space

  • asl_t1_ref – Reference, contrast-enhanced summary of the motion-corrected ASL series in T1w space

  • asl_mask_t1 – ASL mask in T1 space

init_fsl_bbr_wf(use_bbr, asl2t1w_dof, asl2t1w_init, sloppy=False, name='fsl_bbr_wf')[source]

Build a workflow to run FSL’s flirt.

This workflow uses FSL FLIRT to register a ASL image to a T1-weighted structural image, using a boundary-based registration (BBR) cost function. It is a counterpart to init_bbreg_wf(), which performs the same task using FreeSurfer’s bbregister.

The use_bbr option permits a high degree of control over registration. If False, standard, rigid coregistration will be performed by FLIRT. If True, FLIRT-BBR will be seeded with the initial transform found by the rigid coregistration. If None, after FLIRT-BBR is run, the resulting affine transform will be compared to the initial transform found by FLIRT. Excessive deviation will result in rejecting the BBR refinement and accepting the original, affine registration.

Workflow Graph
../_images/aslprep-workflows-asl-registration-3.png

(Source code, png, svg, pdf)

Parameters:

  • use_bbr (bool or None) – Enable/disable boundary-based registration refinement. If None, test BBR result for distortion before accepting.

  • asl2t1w_dof (6, 9 or 12) – Degrees-of-freedom for ASL-T1w registration

  • asl2t1w_init (str, ‘header’ or ‘register’) – If 'header', use header information for initialization of ASL and T1 images. If 'register', align volumes by their centers.

  • name (str, optional) – Workflow name (default: fsl_bbr_wf)

Inputs:

  • in_file – Reference ASL image to be registered

  • t1w_brain – Skull-stripped T1-weighted structural image

  • t1w_dseg – FAST segmentation of t1w_brain

Outputs:

  • itk_asl_to_t1 – Affine transform from ref_asl_brain to T1w space (ITK format)

  • itk_t1_to_asl – Affine transform from T1 space to ASL space (ITK format)

  • out_report – Reportlet for assessing registration quality

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