aslprep.workflows.asl.apply module

Workflows to apply changes to ASL data.

init_asl_cifti_resample_wf(*, metadata: dict, mem_gb: dict, fieldmap_id: str | None = None, omp_nthreads: int = 1, name: str = 'asl_cifti_resample_wf') → Workflow[source]

Resample an ASL series to a CIFTI target space.

This workflow collates a sequence of transforms to resample an ASL series in a single shot, including motion correction and fieldmap correction, if requested.

(Source code)

Parameters:

  • metadata – BIDS metadata for BOLD file.

  • mem_gb

  • fieldmap_id – Fieldmap identifier, if fieldmap correction is to be applied.

  • omp_nthreads – Maximum number of threads an individual process may use.

  • name – Name of workflow (default: bold_volumetric_resample_wf)

Inputs:

  • asl_file – ASL series to resample.

  • bold_ref_file – Reference image to which BOLD series is aligned.

  • target_ref_file – Reference image defining the target space.

  • target_mask – Brain mask corresponding to target_ref_file. This is used to define the field of view for the resampled BOLD series.

  • motion_xfm – List of affine transforms aligning each volume to bold_ref_file. If undefined, no motion correction is performed.

  • boldref2fmap_xfm – Affine transform from bold_ref_file to the fieldmap reference image.

  • fmap_ref – Fieldmap reference image defining the valid field of view for the fieldmap.

  • fmap_coeff – B-Spline coefficients for the fieldmap.

  • fmap_id – Fieldmap identifier, to select correct fieldmap in case there are multiple.

  • boldref2anat_xfm – Affine transform from bold_ref_file to the anatomical reference image.

  • anat2std_xfm – Affine transform from the anatomical reference image to standard space. Leave undefined to resample to anatomical reference space.

Outputs:

  • bold_file – The bold_file input, resampled to target_ref_file space.

  • resampling_reference – An empty reference image with the correct affine and header for resampling further images into the BOLD series’ space.