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:
asl_mask (a pathlike object or string representing an existing file) – ASL mask in native ASL reference space.
csf_tpm (a pathlike object or string representing an existing file) – CSF tissue probability map.
gm_tpm (a pathlike object or string representing an existing file) – Gray matter tissue probability map.
mean_cbf (a pathlike object or string representing an existing file) – Mean CBF from standard CBF calculation.
name_source (a pathlike object or string representing an existing file) – Original asl_file. Used to extract entity information.
t1w_mask (a pathlike object or string representing an existing file) – T1w mask in native space.
wm_tpm (a pathlike object or string representing an existing file) – White matter tissue probability map.
- Optional Inputs:
asl_mask_std (a pathlike object or string representing an existing file) – ASL mask in standard space.
confounds_file (a pathlike object or string representing an existing file) – Confounds file. Will not be defined for GE data.
mean_cbf_basil (a pathlike object or string representing an existing file) – Mean CBF produced by BASIL.
mean_cbf_gm_basil (a pathlike object or string representing an existing file) – GM partial volume corrected CBF with BASIL.
mean_cbf_score (a pathlike object or string representing an existing file) – Mean CBF after SCORE censoring.
mean_cbf_scrub (a pathlike object or string representing an existing file) – Mean CBF after SCRUB denoising.
rmsd_file (a pathlike object or string representing an existing file) – RMSD file. Will not be defined for GE data.
template_mask (a pathlike object or string representing an existing file) – Template mask or image.
tpm_threshold (a float) – Tissue probability threshold for binarizing GM, WM, and CSF masks. (Nipype default value:
0.7
)
- Outputs:
qc_file (a pathlike object or string representing a file) – Qc file .