aslprep.workflows.asl.fit module

Fit workflows for ASLPrep.

get_sbrefs(asl_file: str, entity_overrides: Dict[str, Any], layout: BIDSLayout) → List[str]

Find single-band reference(s) associated with ASL file.

Parameters:

• asl_file – List of absolute paths to ASL files

• entity_overrides – Query parameters to override defaults

• layout – BIDSLayout to query

Returns:

List of absolute paths to sbref files associated with input ASL files, sorted by EchoTime

Return type:

sbref_file

init_asl_fit_wf(*, asl_file: str, m0scan: str | None, use_ge: bool, precomputed: dict = {}, fieldmap_id: str | None = None, omp_nthreads: int = 1, name: str = 'asl_fit_wf') → Workflow

Control the minimal estimation steps for functional preprocessing.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

• asl_file – Path to ASL NIfTI file.

• m0scan – Path to M0 NIfTI file.

• use_ge – If True, the M0 scan (when available) will be prioritized as the volume type for the reference image, as GE deltam volumes exhibit extreme background noise.

• precomputed – Dictionary containing precomputed derivatives to reuse, if possible.

• fieldmap_id – ID of the fieldmap to use to correct this ASL series. If None, no correction will be applied.

Inputs:

• asl_file – ASL series NIfTI file

• t1w_preproc – Bias-corrected structural template image

• t1w_mask – Mask of the skull-stripped template image

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

• anat2std_xfm – List of transform files, collated with templates

• subjects_dir – FreeSurfer SUBJECTS_DIR

• subject_id – FreeSurfer subject ID

• fsnative2t1w_xfm – LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w

• fmap_id – Unique identifiers to select fieldmap files

• fmap – List of estimated fieldmaps (collated with fmap_id)

• fmap_ref – List of fieldmap reference files (collated with fmap_id)

• fmap_coeff – List of lists of spline coefficient files (collated with fmap_id)

• fmap_mask – List of fieldmap masks (collated with fmap_id)

• sdc_method – List of fieldmap correction method names (collated with fmap_id)

Outputs:

• hmc_aslref – ASL reference image used for head motion correction. Minimally processed to ensure consistent contrast with ASL series.

• coreg_aslref – ASL reference image used for coregistration. Contrast-enhanced and fieldmap-corrected for greater anatomical fidelity, and aligned with hmc_aslref.

• asl_mask – Mask of coreg_aslref.

• motion_xfm – Affine transforms from each ASL volume to hmc_aslref, written as concatenated ITK affine transforms.

• aslref2anat_xfm – Affine transform mapping from ASL reference space to the anatomical space.

• aslref2fmap_xfm – Affine transform mapping from ASL reference space to the fieldmap space, if applicable.

• movpar_file – MCFLIRT motion parameters, normalized to SPM format (X, Y, Z, Rx, Ry, Rz)

• rmsd_file – Root mean squared deviation as measured by fsl_motion_outliers [Jenkinson2002].

• dummy_scans – The number of dummy scans declared or detected at the beginning of the series.

init_asl_native_wf(*, asl_file: str, m0scan: str | None = None, fieldmap_id: str | None = None, omp_nthreads: int = 1, name: str = 'asl_native_wf') → Workflow

Apply minimal resampling workflow.

This workflow resamples to aslref space with head motion and susceptibility distortion correction. It also selects the transforms needed to perform further resampling.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

• asl_file – List of paths to NIfTI files.

• m0scan

• fieldmap_id – ID of the fieldmap to use to correct this ASL series. If None, no correction will be applied.

Inputs:

• aslref – ASL reference file

• asl_mask – Mask of ASL reference file

• m0scan – If M0Type is ‘Separate’, then the M0 file will resampled into ASL reference space. Otherwise, this field will be undefined.

• motion_xfm – Affine transforms from each ASL volume to hmc_aslref, written as concatenated ITK affine transforms.

• aslref2fmap_xfm – Affine transform mapping from ASL reference space to the fieldmap space, if applicable.

• fmap_id – Unique identifiers to select fieldmap files

• fmap_ref – List of fieldmap reference files (collated with fmap_id)

• fmap_coeff – List of lists of spline coefficient files (collated with fmap_id)

Outputs:

• asl_minimal – ASL series ready for further resampling. This ASL file will only contain the volumes needed for processing.

• asl_native – ASL series resampled into ASL reference space. Head motion and susceptibility distortion correction will be applied to each file.

• m0scan_native – If M0Type is ‘Separate’, then the M0 file will resampled into ASL reference space. Otherwise, this field will be undefined.

• metadata – Metadata dictionary of ASL series with the shortest echo

• motion_xfm – Motion correction transforms for further correcting asl_minimal. For multi-echo data, motion correction has already been applied, so this will be undefined.