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
- 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
anat_to_template_xfm – List of transform files, collated with templates
template_to_anat_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_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
Brain-mask T1w.
Generate ASL reference image.
Extract averaged, smoothed M0 image and reference image (which is generally the M0 image).
Register ASL to T1w.
Calculate CBF.
Apply the ASL-to-T1w transforms to get T1w-space outputs (passed along to derivatives workflow).
Refine the brain mask.
Warp the ASL brain mask to T1w-space.
CBF plotting workflow.
CBF QC workflow.
Parcellate CBF results.
See also
init_ica_aroma_wf()
init_fmap_wf()
init_pepolar_unwarp_wf()
init_phdiff_wf()
init_syn_sdc_wf()
init_sdc_unwarp_wf()