aslprep.utils.qc module

Functions for evaluating quality of ASL derivatives.

cbf_qei(gm, wm, csf, img, thresh=0.8)

Compute quality evaluation index (QEI) of CBF.

The QEI is based on Dolui et al.[1].

References

coverage(input1, input2)

Estimate the coverage between two binary images.

crosscorr(input1, input2)

Compute cross correlation between two binary images.

dice(input1, input2)

Compute Dice coefficient between the binary objects in two images.

Parameters:

• input1 (str) – Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else.

• input2 (str) – Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else.

Returns:

coef – The Dice coefficient between the object(s) in `input1` and the object(s) in `input2`. It ranges from 0 (no overlap) to 1 (perfect overlap).

Return type:

float

globalcbf(cbf, gm, wm, csf, thresh=0.7)

Compute mean GM, WM, and CSF CBF values.

Parameters:

• cbf (str) – Path to CBF file.

• gm, wm, csf (str) – Paths to GM, WM, and CSF tissue probability maps, in same space and resolution as cbf.

• thresh (float) – Threshold to apply to the TPMs. Default is 0.7.

Returns:

mean_tissue_cbfs – Mean CBF values from binarized versions of the tissue maps.

Return type:

list of float

jaccard(input1, input2)

Compute Jaccard coefficient between the binary objects in two images.

Parameters:

• input1 (str) – Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else.

• input2 (str) – Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else.

Returns:

coef – The Jaccard coefficient between the object(s) in input1 and the object(s) in input2. It ranges from 0 (no overlap) to 1 (perfect overlap).

Return type:

float

negativevoxel(cbf, gm, thresh=0.7)

Compute percentage of negative voxels within grey matter mask.