aslprep.workflows.asl.cbf module
Workflows for calculating CBF.
- init_cbf_compt_wf(name_source, aslcontext, metadata, dummy_vols, scorescrub=False, basil=False, M0Scale=1, smooth_kernel=5, name='cbf_compt_wf')[source]
Create a workflow for CCBF.
- Workflow Graph
- Parameters:
name_source (
str
) – Path to the raw ASL file.aslcontext (
str
) – Path to the aslcontext file associated with the ASL file being processed. Used to set the aslcontext input.metadata (
dict
) – BIDS metadata for asl filescorescrub
basil
M0Scale
smooth_kernel
name (
str
) – Name of workflow (default:cbf_compt_wf
)
- Inputs:
asl_file – asl series NIfTI file, after preprocessing
aslcontext (
str
) – Defined from the parameter.m0scan (
str
or None)m0scan_metadata (
dict
or None)asl_mask – asl mask NIFTI file
t1w_tpms – t1w probability maps
t1w_mask – t1w mask Nifti
t1_asl_xform – t1w to asl transformation file
itk_asl_to_t1 – asl to t1w transformation file
- Outputs:
*cbf – all cbf outputs cbf,score, scrub, pv, and basil
- init_gecbf_compt_wf(name_source, aslcontext, metadata, mem_gb, M0Scale=1, scorescrub=False, basil=False, name='cbf_compt_wf')[source]
Calculate CBF for GE data.
- Workflow Graph
- init_parcellate_cbf_wf(min_coverage=0.5, scorescrub=False, basil=False, mem_gb=0.1, omp_nthreads=1, name='parcellate_cbf_wf')[source]
Parcellate CBF results using a set of atlases.
Atlases are in MNI152NLin6Asym space, but ASLPrep is not guaranteed to generate MNI152NLin6Asym-space derivatives. However, it is guaranteed to generate MNI152NLin2009cAsym derivatives, so this workflow warps the atlases to asl reference space via the path: MNI152NLin6Asym –> MNI152NLin2009cAsym –> anat –> asl.
- Workflow Graph
-
(Source code, png, svg, pdf)
- Parameters:
min_coverage
scorescrub
basil
mem_gb
omp_nthreads
name – Default is “parcellate_cbf_wf”.
- Inputs:
mean_cbf (str)
mean_cbf_score (Undefined or str)
mean_cbf_scrub (Undefined or str)
mean_cbf_basil (Undefined or str)
mean_cbf_gm_basil (Undefined or str)
asl_mask (str)
anat_to_asl_xform (str)
MNI152NLin2009cAsym_to_anat_xform (str) – The transform from MNI152NLin2009cAsym to the subject’s anatomical space.
- Outputs:
atlas_names (list of str) – A list of atlases used for parcellating the CBF results. The list of atlas names is generated by
aslprep.utils.atlas.get_atlas_names()
. The atlases include: “Schaefer117”, “Schaefer217”, “Schaefer317”, “Schaefer417”, “Schaefer517”, “Schaefer617”, “Schaefer717”, “Schaefer817”, “Schaefer917”, “Schaefer1017”, “Glasser”, “Gordon”, and “subcortical” (Tian).mean_cbf_parcellated (list of str)
mean_cbf_score_parcellated (Undefined or list of str) – Only defined if
scorescrub
is True.mean_cbf_scrub_parcellated (Undefined or list of str) – Only defined if
scorescrub
is True.mean_cbf_basil_parcellated (Undefined or list of str) – Only defined if
basil
is True.mean_cbf_gm_basil_parcellated (Undefined or list of str) – Only defined if
basil
is True.