aslprep.workflows.asl.base module

Preprocessing workflows for ASL data.

init_asl_preproc_wf(asl_file)[source]

Perform the functional preprocessing stages of ASLPrep.

Workflow Graph

(Source code)

Parameters:

asl_file – asl series NIfTI file

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

  • template – List of templates to target

  • anat_to_template_xfm – List of transform files, collated with templates

  • template_to_anat_xfm – List of inverse 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 meausres

Notes

  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. If data are multi-echo (which they can’t be), skullstrip the ASL data and perform optimal combination. - Not in GE workflow.

  6. Register ASL to T1w.

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

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

  9. Calculate confounds. - Not in GE workflow.

  10. Calculate CBF.

  11. Refine the brain mask.

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

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

  14. CBF QC workflow.

  15. CBF plotting workflow.

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

  17. Parcellate CBF results.