src.original.fitting.PvH_KB_NKI package

Submodules

src.original.fitting.PvH_KB_NKI.DWI_Examples module

src.original.fitting.PvH_KB_NKI.DWI_functions_standalone module

DWI_functions.py

This module can be used to calculate ADC/IVIM maps. IVIM fitting is done in a segmented fashion: https://doi.org/10.3389/fonc.2021.705964

@authors: s.zijlema, p.vhoudt, k.baas, e.kooreman Group: Uulke van der Heide - NKI

src.original.fitting.PvH_KB_NKI.DWI_functions_standalone.fit_ADCmap_loglinear_standalone(DWIdata, all_bvalues, use_bvalues, size=[])

Function to calculate ADC based on linear regression. Taken from ADC_functions.py but adjusted to also output intercept and removed size input requirement (could be extracted from si_array). The ADC values have been validated with the Philips ADC maps (2022).

Parameters

DWIdata

DWI data

all_bvalues

list or array of b-values that are stored in the data

use_bvalues

list or array of selected b-values selected for calculation.

Returns

ADC calculated ADC and the intercept with the y-axis at b=0 in the same x,y,z coordinates as the original DWI image (i.e. size)

src.original.fitting.PvH_KB_NKI.DWI_functions_standalone.generate_ADC_standalone(DWIdata, bvalues, bmin: int = 150, bmax: int = 1000, specificBvals: list = [])

Function to create an ADC map from DWI data. Required input is a numpy array with the data and the corresponding b-values

Example use: generate_ADC(data, bvalues)

Parameters

DWIdata: numpy array

DWI data

bvalues: list

bvalues corresponding to the data

bmin/bmax (optional)

Used to select range of b-values that you want to include to calculate the ADC. Not used when specificBvals is defined.

specificBvals (optional)

List of b-values that should be used for ADC map calculation. If set, bmin/bmax options are not used.

Returns

ADClog

ADC map

b0_intercept

Map with y-intercepts (b=0) of ADC fit

bvalues

b-values that matched the criteria

src.original.fitting.PvH_KB_NKI.DWI_functions_standalone.generate_IVIMmaps_standalone(DWIdata, bvalues, bminADC=150, bmaxADC=1000, bmaxDstar=50)

Function to calculate IVIM maps (perfusion fraction and D*). NOTE: D* is calculated using only the lowest two b-values.

Example use: generate_IVIMmaps(data, bvalues)

Parameters

DWIdata: numpy array

DWI data

bvalues: list

bvalues corresponding to the data

bminADC/bmaxADC (optional)

Used to select the range of b-values for ADC calculation.

bmaxDstar (optional)

Used to select the b-values for D* calculation.

outputOptions

[‘ADC’,’f’,’D*’] (default) will output the ADC, f, and D*.

src.original.fitting.PvH_KB_NKI.DWI_functions_standalone.select_b_values_standalone(all_bvalues, bmin=0, bmax=inf, specificBvals: list = [])

Find b-values and their indices between bmin and bmax of a scan (bmin <= b <= b max) or of b-values that are defined in specificBvals. If specificBvals is defined, only b-values are returned that are acquired in the scan AND are present in specificBvals.

Parameters

all_bvalueslist of int

All b values that are in the data in the order that they are stored

bminint

Minimal b-value.

bmaxint

Maximal b-value.

specificBvalslist

List of b-values.

Returns

bvalueindexlist of int

Indices of b-values between bmin and bmax.

bvalueslist of int

B-values between bmin and bmax.

Module contents