Overview of code collection

Technique	Category	Subcategory (link to source code)	Notes	Subfolder	Authors	Institution	function/module name	doi	Tester	Test status (empty/in-progress/complete)
DCE	Bolus arrival time	piecewise linear quadratic function	Cheong et al (DOI: 10.1088/0031-9155/48/5/403)	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	BAT_linquad	nan	tbd	nan
DCE	Bolus arrival time	fitting Kety (Tofts) model to first third of the curve	nan	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	BAT_kety	nan	tbd	nan
DCE	Input Functions	load AIF	load from txt	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	read_AIF	https://doi.org/10.21105/joss.03523	tbd	nan
DCE	Input Functions	Parker AIF	nan	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	compute_population_AIF	https://doi.org/10.21105/joss.03523	JK/PvH	completed
DCE	Input Functions	patient-specific AIF	constructed from time-concentration data	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	patientSpecific	nan	tbd	nan
DCE	Input Functions	Parker AIF	Parker AIF, Parker-like AIF	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Parker	nan	JK/PvH	completed
DCE	Input Functions	Manning AIF	Manning et al (https://doi.org/10.1002/mrm.28833)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	ManningFast, ManningSlow	nan	tbd	completed
DCE	Input Functions	Heye AIF	Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Heye	nan	tbd	completed
DCE	Input Functions	AIF parameterization	nan	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	Cosine4AIF, Cosine8AIF	https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9	tbd	nan
DCE	Input Functions	Head-and-neck population AIF	Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433)	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	aifPopHN	nan	tbd	nan
DCE	Input Functions	Parker AIF	nan	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	aifPopPMB	nan	tbd	nan
DCE	Input Functions	load AIF	from txt	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	loadStandard	nan	tbd	nan
DCE	Input Functions	AIF parameterization	fit gamma-variate function	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	gammaVariateFit	nan	tbd	nan
DCE	Input Functions	Georgiou AIF	Georgiou et al (DOI: 10.1002/mrm.27524)	PvH_NKI	Petra van Houdt	the Netherlands Cancer Institute, the Netherlands	GeorgiouAIF	nan	JK/PvH	completed
DCE	Input Functions	Parker AIF	nan	PvH_NKI	Petra van Houdt	the Netherlands Cancer Institute, the Netherlands	ParkerAIF	nan	JK/PvH	completed
DCE	Input Functions	Parker AIF	nan	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	AIF, variableAIF	nan	JK/PvH	completed
DCE	Input Functions	preclinical AIF	McGrath et al (DOI: 10.1002/mrm.21959)	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	preclinicalAIF	nan	JK/PvH	completed
DCE	Miscellaneous	enhancement detection	check for enhancement	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	enhance	nan	tbd	nan
DCE	Parameter derivation	iAUC	nan	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	compute_IAUC	https://doi.org/10.21105/joss.03523	tbd	nan
DCE	Pharmacokinetic models	Tofts	NLLS fitting (+forward model)	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	tofts_integral, fit_tofts_model	nan	tdd	nan
DCE	Pharmacokinetic models	extended Tofts	NLLS fitting (+forward model)	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	ext_tofts_integral, fit_tofts_model	nan	tbd	nan
DCE	Pharmacokinetic models	Tofts	NLLS fitting (+ forward model)	LCB_BNI_USA	Laura Bell	Barrow Neurological Institute, USA	tofts_model, fit_tofts	nan	ST/OGC	completed
DCE	Pharmacokinetic models	2-cmp exchange	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	TwoCXM	nan	MJT	completed
DCE	Pharmacokinetic models	2-cmp uptake	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	TwoCUM	nan	MJT	completed
DCE	Pharmacokinetic models	AATH	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	AATH	nan	tbd	nan
DCE	Pharmacokinetic models	extended Tofts	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	ExtKety	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Patlak	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	Patlak	nan	MJT	completed
DCE	Pharmacokinetic models	Tofts	forward model	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	Kety	nan	ST/OGC	completed
DCE	Pharmacokinetic models	2-cmp exchange	LLSQ fitting (+forward model)	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	two_cxm_model	https://doi.org/10.21105/joss.03523	MJT	completed
DCE	Pharmacokinetic models	2-cmp filtration	LLSQ fitting (+forward model)	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	two_cfm_model	https://doi.org/10.21105/joss.03523	tbd	nan
DCE	Pharmacokinetic models	active uptake and efflux (AUEM)	LLSQ fitting (+forward model)	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	active_uptake_model	https://doi.org/10.21105/joss.03523	tbd	nan
DCE	Pharmacokinetic models	dual-inlet general model	LLSQ fitting (+forward model)	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	dibem	https://doi.org/10.21105/joss.03523	tbd	nan
DCE	Pharmacokinetic models	extended Tofts	LLSQ fitting (+forward model)	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	tofts_model	https://doi.org/10.21105/joss.03523	ST/OGC	completed
DCE	Pharmacokinetic models	2-cmp exchange	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	TCXM, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	2-cmp exchange	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	TCXM, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	2-cmp uptake	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	TCUM, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	2-cmp uptake	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	TCUM, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	extended Tofts	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	ExtendedTofts, EnhToPKP, ConcToPKP	nan	ST/OGC	completed
DCE	Pharmacokinetic models	extended Tofts	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	ExtendedTofts, EnhToPKP, ConcToPKP	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Patlak	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Patlak, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	Patlak	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Patlak, EnhToPKP, ConcToPKP	nan	MJT	completed
DCE	Pharmacokinetic models	Patlak	LLSQ fitting	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	PatlakLinear	nan	MJT	completed
DCE	Pharmacokinetic models	steady-state vp	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	SteadyStateVp, EnhToPKP, ConcToPKP	nan	tbd	nan
DCE	Pharmacokinetic models	steady-state vp	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	SteadyStateVp, EnhToPKP, ConcToPKP	nan	tbd	nan
DCE	Pharmacokinetic models	Tofts	NLLS fitting to concentration values (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Tofts, EnhToPKP, ConcToPKP	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Tofts	NLLS fitting to signal incl. water exchange (incl forward model)	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	Tofts,EnhToPKP, ConcToPKP	nan	ST/OGC	completed
DCE	Pharmacokinetic models	extended Tofts	NLLS fitting (+forward model)	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	fit_tofts_model	nan	ST/OGC	completed
DCE	Pharmacokinetic models	2-cmp exchange	LLSQ fitting (+ forward model)	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	twoCXM, fitToModelLLSQ	nan	MJT	completed
DCE	Pharmacokinetic models	extended Tofts	NLLS fitting (+ forward model)	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	ETM, fitToModelNLLS, fitToModelNLLS_parallel	nan	ST/OGC	completed
DCE	Pharmacokinetic models	extended Tofts	LLSQ fitting (+ forward model)	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	ETM, fitToModelLLSQ	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Tofts	NLLS fitting (+ forward model)	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, Norway	TM, fitToModelNLLS, fitToModelNLLS_parallel	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Tofts	LLSQ fitting (+ forward model)	OGJ_OsloU_NOR	Ole Gunnar Johansen	University of Oslo, NOR	TM, fitToModelLLSQ	nan	ST/OGC	completed
DCE	Pharmacokinetic models	1-cmp	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	OneCompartment	nan	tbd	nan
DCE	Pharmacokinetic models	dual-inlet 1-cmp	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	DualInletOneCompartment	nan	tbd	nan
DCE	Pharmacokinetic models	dual-inlet ext Tofts	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	DualInletExtendedTofts	nan	tbd	nan
DCE	Pharmacokinetic models	dual-inlet high-flow 2-cmp Gadoxetate	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	DualInletconc_HF2CGM	nan	tbd	nan
DCE	Pharmacokinetic models	extended Tofts	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	ExtendedTofts	nan	ST/OGC	completed
DCE	Pharmacokinetic models	Tofts	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	Tofts	nan	ST/OGC	completed
DCE	Pharmacokinetic models	high flow 2-cmp Gadoxetate	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	nan	nan	tbd	nan
DCE	Pharmacokinetic models	Patlak	forward model	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	PatlakModel	nan	MJT	completed
DCE	Signal to Concentration	SPGR	two-steps: S->R1, R1->C	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	r1eff_to_conc, dce_to_r1eff	nan	tbd	nan
DCE	Signal to Concentration	SPGR or GE-EPI	nan	LCB_BNI_USA	Laura Bell	Barrow Neurological Institute, USA	signal_to_conc, estimate_delta_R1	nan	LK	completed
DCE	Signal to concentration	SPGR	reverse C->S also available	LEK_UoEdinburgh	Lucy Kershaw	University of Edinburgh, UK	SI2Conc	nan	LK	completed
DCE	Signal to concentration	SPGR	reverse C->S also available	MB_QBI_UoManchester_UK	Michael Berks	University of Manchester, UK	signal_to_concentration	https://doi.org/10.21105/joss.03523	LK	completed
DCE	Signal to concentration	SPGR	two steps: S-> enhancement, enhancement -> C; reverse C->S also available	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	sign_to_enh, enh_to_conc	nan	LK	completed
DCE	Signal to concentration	SPGR	two steps: S->R1, R1 -> C; reverse C->S also available	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	dce_to_r1eff, r1eff_to_conc	nan	LK	completed
DCE	Signal to concentration	SPGR	reverse R1->C also available	ST_USydAUS_DCE	Sirisha Tadimalla	University of Sydney, Australia	signals2conc	nan	LK	completed
DCE	T1	VFA	nonlinear	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	fit_R1	nan	tbd	nan
DCE	T1	VFA	despot	McGill_VFA	Zaki Ahmed	McGill University, Canada	despot	nan	MJT	completed
DCE	T1	VFA	novifast	McGill_VFA	Zaki Ahmed	McGill University, Canada	novifast	nan	MJT	completed
DCE	T1	DESPOT1-HIFI	Fit any combination of (IR-)SPGR scans to estimate T1	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	HIFI	nan	MJT	in-progress
DCE	T1	VFA	linear	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	VFALinear	nan	MJT	complete
DCE	T1	VFA	nonlinear	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	VFANonlinear	nan	MJT	complete
DCE	T1	VFA	two flip angles	MJT_UoEdinburgh_UK	Michael Thrippleton	University of Edinburgh, UK	VFA2Points	nan	tbd	nan
DCE	T1	VFA	two flip angles (linear)	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	R1_two_fas	nan	MJT	competed
DCE	T1	VFA	nonlinear	OG_MO_AUMC_ICR_RMH	Oliver Gurney-Champion, Matthew Orton	Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK	R1_VFA	nan	MJT	competed
DCE	T1	VFA	linear	ST_Sydney_AUS_T1	Sirisha Tadimalla	University of Sydney, Australia	VFAT1mapping	nan	MJT	completed
DCE	T1	VFA	nonlinear	ST_Sydney_AUS_T1	Sirisha Tadimalla	University of Sydney, Australia	VFAT1mapping	nan	MJT	completed
DCE/DSC	AIF deconvolution	Volterra discretization with L-curve criterion	nan	SR_TBG_BNI_PhoenixUSA	Sudarshan Ragunathan, Laura Bell	Barrow Neurological Institute, USA	AIFdeconvolution	nan	JA	completed
DCE/DSC	Miscellaneous	calculate SNR	nan	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	signal_to_noise_ratio	nan	tbd	nan
DCE/DSC	Miscellaneous	calculate enhancement ratio	nan	DS_BW_VanderBiltUMC_USA	David Smith, Brian Welch	VanderBilt University Medical Center, USA	signal_enhancement_ratio	nan	tbd	nan
DSC	Input Functions	automatic AIF selection	fully automatic, semi-automatic	JBJA_GUSahlgrenskaSWE	Jesper Browall, Jonathan Arvidsson	Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden	AIF_selection_automatic.py	DOI: 10.1002/mrm.20759	tbd	nan
DSC	Leakage correction	BSW	nan	SR_TBG_BNI_PhoenixUSA	Sudarshan Ragunathan, Laura Bell	Barrow Neurological Institute, USA	BSWleakagecorr	nan	SR	in-progress
DSC	Parameter derivation	CBV,CBF,MTT	nan	SR_TBG_BNI_PhoenixUSA	Sudarshan Ragunathan, Laura Bell	Barrow Neurological Institute, USA	DSCparameters	nan	tbd	nan
DSC	Signal to deltaR2*	single echo	nan	LCB_BNI_USA	Laura Bell	Barrow Neurological Institute, USA	nan	estimate_delta_R2s	tbd	nan
DSC	Signal to deltaR2*	dual echo	nan	LCB_BNI_USA	Laura Bell	Barrow Neurological Institute, USA	nan	estimate_delta_R2s, estimate_delta_R2s_dual_echo	tbd	nan
DSC	Signal to R2*	dual echo	nan	LCB_BNI_USA	Laura Bell	Barrow Neurological Institute, USA	nan	estimate_R2s	tbd	nan