aslprep.workflows.asl.base module

Preprocessing workflows for ASL data.

init_asl_wf(*, asl_file: str, precomputed: dict = {}, fieldmap_id: str | None = None)

Perform the functional preprocessing stages of ASLPrep.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

• asl_file – ASL NIfTI file

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

• fieldmap_id – ID of the fieldmap to use to correct this BOLD 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)

• t1w_tpms – List of tissue probability maps in T1w space

• 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)

• template – List of templates to target

• anat2std_xfm – List of transform files, collated with templates

Outputs:

• asl_t1 – asl series, resampled to T1w space

• asl_mask_t1 – asl series mask in T1w space

• asl_std – asl series, resampled to template space

• asl_mask_std – asl series mask in template space

• confounds – TSV of confounds

• cbf_ts_t1 – cbf times series in T1w space

• mean_cbf_t1 – mean cbf in T1w space

• cbf_ts_score_t1 – scorecbf times series in T1w space

• mean_cbf_score_t1 – mean score cbf in T1w space

• mean_cbf_scrub_t1, mean_cbf_gm_basil_t1, mean_cbf_basil_t1 – scrub, parital volume corrected and basil cbf in T1w space

• cbf_ts_std – cbf times series in template space

• mean_cbf_std – mean cbf in template space

• cbf_ts_score_std – scorecbf times series in template space

• mean_cbf_score_std – mean score cbf in template space

• mean_cbf_scrub_std, mean_cbf_gm_basil_std, mean_cbf_basil_std – scrub, parital volume corrected and basil cbf in template space

• qc_file – quality control measures

Notes

Note that anat2std_xfm, std_space, std_resolution, std_cohort, std_t1w and std_mask are treated as single inputs. In order to resample to multiple target spaces, connect these fields to an iterable.

1. Brain-mask T1w.

2. Generate initial ASL reference image. I think this is just the BOLD reference workflow from niworkflows, without any modifications for ASL data. I could be missing something. - Not in GE workflow. - In the GE workflow, the reference image comes from the M0 scan.

3. Motion correction. - Outputs the HMC transform and the motion parameters. - Not in GE workflow.

4. Susceptibility distortion correction. - Outputs the SDC transform. - Not in GE workflow.

5. Register ASL to T1w.

6. Apply the ASL-to-T1w transforms to get T1w-space outputs (passed along to derivatives workflow).

7. Apply the ASL-to-ASLref transforms to get native-space outputs. - Not in GE workflow.

8. Calculate confounds. - Not in GE workflow.

9. Calculate CBF.

10. Refine the brain mask.

11. Generate distortion correction report. - Not in GE workflow.

12. Apply ASL-to-template transforms to get template-space outputs.

13. CBF QC workflow.

14. CBF plotting workflow.

15. Generate carpet plots. - Not in GE workflow.

16. Parcellate CBF results.