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