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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