aslprep.workflows.asl.cbf module

Workflows for calculating CBF.

init_cbf_wf(*, name_source, processing_target, aslcontext, metadata, m0scan_metadata=None, scorescrub=False, basil=False, m0_scale=1, smooth_kernel=5, name='cbf_wf')[source]

Create a workflow for CCBF.

Workflow Graph

(Source code)

Parameters:

  • name_source (str) – Path to the raw ASL file.

  • metadata (dict) – BIDS metadata for asl file. List-type fields in this dict have not been reduced based on selected volumes, so this should only be used for metadata that is not affected by volume selection.

  • scorescrub

  • basil

  • m0_scale

  • smooth_kernel

  • name (str) – Name of workflow (default: cbf_wf)

Inputs:

  • asl_file – asl series NIfTI file, after preprocessing

  • aslcontext (str)

  • metadata (dict) – Metadata dictionary associated with asl_file, after preprocessing. List-type fields in this dict have been reduced based on selected volumes, so this is the dictionary that should be used to select volumes.

  • m0scan (str or None) – An M0 scan (if available as a separate file) in aslref space.

  • m0scan_metadata (dict or None)

  • asl_mask – asl mask NIFTI file

  • t1w_tpms – t1w probability maps

  • t1w_mask – t1w mask Nifti

  • aslref2anat_xfm – asl to t1w transformation file

Outputs:

*cbf – all cbf outputs cbf,score, scrub, pv, and basil

init_load_atlases_wf(name='load_atlases_wf')[source]

Collect atlases and copy them to the sourcedata/atlases directory.

Workflow Graph

(Source code)

Parameters:

%(name)s – Default is “load_atlases_wf”.

Outputs:

  • atlas_names

  • atlas_files

  • atlas_labels_files

init_parcellate_cbf_wf(cbf_3d, min_coverage=0.5, 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
../_images/aslprep-workflows-asl-cbf-3.png

(Source code, png, svg, pdf)

Parameters:

  • min_coverage

  • scorescrub

  • basil

  • mem_gb

  • omp_nthreads

  • name – Default is “parcellate_cbf_wf”.

Inputs:

  • source_file (str)

  • 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)

  • aslref2anat_xfm (str)

  • mni2009c2anat_xfm (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.select_atlases(). The atlases include: “4S156Parcels”, “4S256Parcels”, “4S356Parcels”, “4S456Parcels”, “4S556Parcels”, “4S656Parcels”, “4S756Parcels”, “4S856Parcels”, “4S956Parcels”, “4S1056Parcels”, “Glasser”, “Gordon”, “Tian”, and “HCP”.

  • 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.