aslprep.workflows.asl.registration module
Workflows for registering ASL data.
- init_asl_reg_wf(use_bbr, asl2t1w_dof, asl2t1w_init, sloppy=False, write_report=True, name='asl_reg_wf')[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
- Parameters:
use_bbr (
bool
or None) – Enable/disable boundary-based registration refinement. IfNone
, 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 GBomp_nthreads (
int
) – Maximum number of threads an individual process may usename (
str
) – Name of workflow (default:asl_reg_wf
)use_compression (
bool
) – Save registered ASL series as.nii.gz
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 unwarpedt1w_brain – Skull-stripped
t1w_preproc
t1w_dseg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
- Outputs:
aslref_to_anat_xfm – Affine transform from
ref_asl_brain
to T1 space (ITK format)anat_to_aslref_xfm – 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, is_multi_pld=False, scorescrub=False, basil=False, generate_reference=True, output_t1space=False, use_compression=True, name='asl_t1_trans_wf')[source]
Sample ASL into T1w space with a single-step resampling of the original ASL series.
TODO: Allow hmc_xforms and fieldwarp to be “identity”.
The workflow uses BBR.
- Workflow Graph
- Parameters:
- 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 unwarpedref_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 (list of str) – Individual 3D ASL volumes, not motion corrected. The individual volumes allow MultiApplyTransforms to apply that volume’s specific transforms (namely, the HMC transform, since the other transforms are the same across volumes).
hmc_xforms – List of affine transforms aligning each volume to
ref_image
in ITK formataslref_to_anat_xfm – 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
aslref_t1 – 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’sbbregister
.The
use_bbr
option permits a high degree of control over registration. IfFalse
, standard, rigid coregistration will be performed by FLIRT. IfTrue
, FLIRT-BBR will be seeded with the initial transform found by the rigid coregistration. IfNone
, 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
- Parameters:
use_bbr (
bool
or None) – Enable/disable boundary-based registration refinement. IfNone
, 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:
aslref_to_anat_xfm – Affine transform from
ref_asl_brain
to T1w space (ITK format)anat_to_aslref_xfm – 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)