aslprep.interfaces.qc module

Interfaces for calculating CBF.

class ComputeCBFQC(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Calculate a series of CBF quality control metrics for GE data.

compute qc from confound regressors and cbf maps, coregistration and regsitration indexes

Mandatory Inputs:

  • in_aslmask (a pathlike object or string representing an existing file) – Asl mask in native space.

  • in_csf (a pathlike object or string representing an existing file) – Csf tissue probability map.

  • in_greyM (a pathlike object or string representing an existing file) – Grey matter tissue probability map.

  • in_meancbf (a pathlike object or string representing an existing file) – Cbf img.

  • in_t1mask (a pathlike object or string representing an existing file) – T1wmask in native space .

  • in_whiteM (a pathlike object or string representing an existing file) – White matter tissue probability map.

  • name_source (a pathlike object or string representing an existing file) – Original asl_file. Used to extract entity information.

Optional Inputs:

  • in_aslmaskstd (a pathlike object or string representing an existing file) – Asl mask in native space.

  • in_avgscore (a pathlike object or string representing an existing file) – Cbf img.

  • in_basil (a pathlike object or string representing an existing file) – Cbf img.

  • in_confmat (a pathlike object or string representing an existing file) – Confounds file. Will not be defined for GE data.

  • in_pvc (a pathlike object or string representing an existing file) – Cbf img.

  • in_scrub (a pathlike object or string representing an existing file) – Cbf img.

  • in_templatemask (a pathlike object or string representing an existing file) – Template mask or image.

  • rmsd_file (a pathlike object or string representing an existing file) – RMSD file. Will not be defined for GE data.

  • tpm_threshold (a float) – Typically 0.7 for non-GE data and 0.8 for GE data.

Outputs:

qc_file (a pathlike object or string representing a file) – Qc file .