aslprep.workflows.asl.gecbf module

CBF-processing workflows for GE data.

init_asl_gepreproc_wf(asl_file)[source]

Manage the functional preprocessing stages of ASLPrep, for GE data.

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_asec – Segmentation of structural image, done with FreeSurfer.

  • t1w_aparc – Parcellation of structural image, done with FreeSurfer.

  • t1w_tpms – List of tissue probability maps in T1w space

  • template – List of templates to target

  • anat2std_xfm – List of transform files, collated with templates

  • std2anat_xfm – List of inverse transform files, collated with templates

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • subject_id – FreeSurfer subject ID

  • t1w2fsnative_xfm – LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space

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

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

  • surfaces – asl series, resampled to FreeSurfer surfaces

  • asl_cifti – asl CIFTI image

  • cifti_variant – combination of target spaces for asl_cifti

  • cbf_t1 – cbf times series in T1w space

  • meancbf_t1 – mean cbf in T1w space

  • scorecbf_t1 – scorecbf times series in T1w space

  • avgscorecbf_t1 – mean score cbf in T1w space

  • scrub_t1, pv_t1, basil_t1 – scrub, parital volume corrected and basil cbf in T1w space

  • cbf_std – cbf times series in template space

  • meancbf_std – mean cbf in template space

  • scorecbf_std – scorecbf times series in template space

  • avgscorecbf_std – mean score cbf in template space

  • scrub_std, pv_std, basil_std – scrub, parital volume corrected and basil cbf in template space

  • qc_file – quality control meausres

Notes

  1. Brain-mask T1w.

  2. Extract averaged, smoothed M0 image and reference image (which is generally the M0 image).

  3. Estimate transforms from ASL to T1w.

  4. Compute CBF.

  5. Co-register the reference ASL image to T1w-space. (what about Step 3?)

  6. Refine the ASL brain mask.

  7. Warp the ASL brain mask to T1w-space.

  8. CBF plotting workflow.

  9. CBF QC workflow.

  10. Parcellate CBF results.

See also