From 6e7c3b21796956f7dd8d624d7b305ca960dccf70 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 14:44:57 +0000 Subject: [PATCH 01/21] naming --- doc/code_contributions_record.csv | 2 +- doc/convert_to_md.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 doc/convert_to_md.py diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 104c0e96..c7f5fc8f 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -1,5 +1,5 @@ Technique,Category,Subcategory,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,,tbd, +DCE,Bolus arrival time,[piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, DCE,Bolus arrival time,fitting Kety (Tofts) model to first third of the curve,,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, 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, DCE,Input Functions,Parker AIF,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_population_AIF,https://doi.org/10.21105/joss.03523,JK/PvH,completed diff --git a/doc/convert_to_md.py b/doc/convert_to_md.py new file mode 100644 index 00000000..9a285ad3 --- /dev/null +++ b/doc/convert_to_md.py @@ -0,0 +1,5 @@ +import pandas as pd + +df = pd.read_csv('./code_contributions_record.csv') +with open('code_contributions_record.md', 'w') as md: + df.to_markdown(buf=md, index=False) \ No newline at end of file From 3bf1dde54491d4d939df9808e639403b0a42b8c8 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 14:46:03 +0000 Subject: [PATCH 02/21] naming --- doc/code_contributions_record.md | 89 ++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 doc/code_contributions_record.md diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md new file mode 100644 index 00000000..159fdab6 --- /dev/null +++ b/doc/code_contributions_record.md @@ -0,0 +1,89 @@ +| Technique | Category | Subcategory | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | +|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| +| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | nan | 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 | \ No newline at end of file From 2157dff4868ee60b58e3b49c1c40eaba956a8e83 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:09:58 +0000 Subject: [PATCH 03/21] naming --- .github/workflows/ci.yml | 28 ++++++++++ doc/code_contributions_record.md | 89 -------------------------------- 2 files changed, 28 insertions(+), 89 deletions(-) delete mode 100644 doc/code_contributions_record.md diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 76c9bf65..e4bee1dd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,6 +8,34 @@ on: - pull_request jobs: + + convert: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + python-version: [3.8] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + pip install wheel pandas + pip install wheel tabulate + - name: Run script to convert table + run: | + python doc/convert_to_md.py + - name: Commit md file + run: | + git config --global user.name 'OSIPI' + git config --global user.email 'OSIPI@users.noreply.github.com' + git commit -am "code_contributions_record.md" + git push + build: runs-on: ${{ matrix.os }} diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md deleted file mode 100644 index 159fdab6..00000000 --- a/doc/code_contributions_record.md +++ /dev/null @@ -1,89 +0,0 @@ -| Technique | Category | Subcategory | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | -|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| -| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | nan | 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 | \ No newline at end of file From 05b342991ff51c6be1476acd7bcfa5060dd060e1 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:36:12 +0000 Subject: [PATCH 04/21] naming --- doc/convert_to_md.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/convert_to_md.py b/doc/convert_to_md.py index 9a285ad3..93d53261 100644 --- a/doc/convert_to_md.py +++ b/doc/convert_to_md.py @@ -1,5 +1,5 @@ import pandas as pd -df = pd.read_csv('./code_contributions_record.csv') -with open('code_contributions_record.md', 'w') as md: +df = pd.read_csv('doc/code_contributions_record.csv') +with open('doc/code_contributions_record.md', 'w') as md: df.to_markdown(buf=md, index=False) \ No newline at end of file From 9f44b02f655158f87cddc47fe8b51060cdb68f6f Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:39:58 +0000 Subject: [PATCH 05/21] naming --- .github/workflows/ci.yml | 53 ++++++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e4bee1dd..985f89a4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,33 +31,34 @@ jobs: python doc/convert_to_md.py - name: Commit md file run: | + git add doc/convert_to_md.py git config --global user.name 'OSIPI' git config --global user.email 'OSIPI@users.noreply.github.com' - git commit -am "code_contributions_record.md" + git commit -am "commit code_contributions_record.md" git push - build: - - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest, macos-latest, windows-latest] - python-version: [3.8] - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install wheel flake8 pytest codecov - pip install ".[test]" - - name: Test with pytest - run: | - coverage run -m pytest - - name: Upload coverage to codecov - run: | - codecov +# build: +# +# runs-on: ${{ matrix.os }} +# strategy: +# matrix: +# os: [ubuntu-latest, macos-latest, windows-latest] +# python-version: [3.8] +# +# steps: +# - uses: actions/checkout@v2 +# - name: Set up Python ${{ matrix.python-version }} +# uses: actions/setup-python@v2 +# with: +# python-version: ${{ matrix.python-version }} +# - name: Install dependencies +# run: | +# python -m pip install --upgrade pip +# pip install wheel flake8 pytest codecov +# pip install ".[test]" +# - name: Test with pytest +# run: | +# coverage run -m pytest +# - name: Upload coverage to codecov +# run: | +# codecov From f1dc4704bb7547265fa98fd55007763b0f73d5e7 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:40:49 +0000 Subject: [PATCH 06/21] update --- .github/workflows/jupyterbook.yml | 94 +++++++++++++++---------------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/.github/workflows/jupyterbook.yml b/.github/workflows/jupyterbook.yml index 1a4007d8..b563067e 100644 --- a/.github/workflows/jupyterbook.yml +++ b/.github/workflows/jupyterbook.yml @@ -7,50 +7,50 @@ on: - develop # This job installs dependencies, build the book, and pushes it to `gh-pages` -jobs: - build-and-deploy-book: - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest] - python-version: [3.8] - steps: - - uses: actions/checkout@v2 - - # Install dependencies - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - pip install wheel pytest - pip install -r notebooks/requirements.txt - pip install . - - - name: Test with pytest - run: | - pytest . - - # Build the book - - name: Build the book - run: | - jupyter-book build notebooks/ - touch notebooks/_build/html/.nojekyll - - - name: Re-organize files - run: | - mkdir out - mv notebooks/_build/html out/docs - mv test out/test - - # Deploy the book's HTML to another repo - - name: publish:starters - uses: cpina/github-action-push-to-another-repository@master - env: - API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }} - with: - source-directory: 'out' - destination-github-username: 'OSIPI' - destination-repository-name: 'DCE-DSC-MRI_TestResults' - user-email: zaki@live.ca \ No newline at end of file +#jobs: +# build-and-deploy-book: +# runs-on: ${{ matrix.os }} +# strategy: +# matrix: +# os: [ubuntu-latest] +# python-version: [3.8] +# steps: +# - uses: actions/checkout@v2 +# +# # Install dependencies +# - name: Set up Python ${{ matrix.python-version }} +# uses: actions/setup-python@v1 +# with: +# python-version: ${{ matrix.python-version }} +# - name: Install dependencies +# run: | +# pip install wheel pytest +# pip install -r notebooks/requirements.txt +# pip install . +# +# - name: Test with pytest +# run: | +# pytest . +# +# # Build the book +# - name: Build the book +# run: | +# jupyter-book build notebooks/ +# touch notebooks/_build/html/.nojekyll +# +# - name: Re-organize files +# run: | +# mkdir out +# mv notebooks/_build/html out/docs +# mv test out/test +# +# # Deploy the book's HTML to another repo +# - name: publish:starters +# uses: cpina/github-action-push-to-another-repository@master +# env: +# API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }} +# with: +# source-directory: 'out' +# destination-github-username: 'OSIPI' +# destination-repository-name: 'DCE-DSC-MRI_TestResults' +# user-email: zaki@live.ca \ No newline at end of file From 49d4c6e45f1e19912f947c176b0d030b3a7bd11b Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:42:46 +0000 Subject: [PATCH 07/21] update --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 985f89a4..576db5a0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: python doc/convert_to_md.py - name: Commit md file run: | - git add doc/convert_to_md.py + git add doc/code_contributions_record.md git config --global user.name 'OSIPI' git config --global user.email 'OSIPI@users.noreply.github.com' git commit -am "commit code_contributions_record.md" From 58380c71e456ed709fc681f84b38293ea11c40a5 Mon Sep 17 00:00:00 2001 From: OSIPI Date: Thu, 3 Nov 2022 16:43:15 +0000 Subject: [PATCH 08/21] commit code_contributions_record.md --- doc/code_contributions_record.md | 89 ++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 doc/code_contributions_record.md diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md new file mode 100644 index 00000000..159fdab6 --- /dev/null +++ b/doc/code_contributions_record.md @@ -0,0 +1,89 @@ +| Technique | Category | Subcategory | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | +|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| +| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | nan | 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 | \ No newline at end of file From fc35a04d67b73ba77eca7208b72b5d3a79aba2a4 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:45:25 +0000 Subject: [PATCH 09/21] update --- doc/code_contributions_record.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index c7f5fc8f..1322848a 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -1,4 +1,4 @@ -Technique,Category,Subcategory,Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) +Technique,Category,Subcategory (link),Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) DCE,Bolus arrival time,[piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, DCE,Bolus arrival time,fitting Kety (Tofts) model to first third of the curve,,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, 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, From d703cccf5dc885a8d32b4f4f55269f3c143aef43 Mon Sep 17 00:00:00 2001 From: OSIPI Date: Thu, 3 Nov 2022 16:48:03 +0000 Subject: [PATCH 10/21] commit code_contributions_record.md --- doc/code_contributions_record.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md index 159fdab6..bc82170e 100644 --- a/doc/code_contributions_record.md +++ b/doc/code_contributions_record.md @@ -1,4 +1,4 @@ -| Technique | Category | Subcategory | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | +| Technique | Category | Subcategory (link) | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | |:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| | DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | From 0c8e9c3779048b2514e80ddfe213692d90c45451 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:55:50 +0000 Subject: [PATCH 11/21] Rename code_contributions_record.md to readme.md --- doc/{code_contributions_record.md => readme.md} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename doc/{code_contributions_record.md => readme.md} (99%) diff --git a/doc/code_contributions_record.md b/doc/readme.md similarity index 99% rename from doc/code_contributions_record.md rename to doc/readme.md index bc82170e..0c14c8eb 100644 --- a/doc/code_contributions_record.md +++ b/doc/readme.md @@ -86,4 +86,4 @@ | 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 | \ No newline at end of file +| DSC | Signal to R2* | dual echo | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_R2s | tbd | nan | From 5f5e763fcbaba945bb126ca64e75ee1cb2b3cf0c Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:57:18 +0000 Subject: [PATCH 12/21] Delete readme.md --- doc/readme.md | 89 --------------------------------------------------- 1 file changed, 89 deletions(-) delete mode 100644 doc/readme.md diff --git a/doc/readme.md b/doc/readme.md deleted file mode 100644 index 0c14c8eb..00000000 --- a/doc/readme.md +++ /dev/null @@ -1,89 +0,0 @@ -| Technique | Category | Subcategory (link) | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | -|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| -| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | nan | 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 | From 5a8cc4ae4b8518166134ba201700dffc98e74e78 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 16:57:27 +0000 Subject: [PATCH 13/21] update --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ed7cf1ed..cc468afb 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ A summary of the repository structure is shown below. More detailed information ``` OSIPI/DCE-DSC-MRI_CodeCollection ├── doc -│ └── code_contributions_record.csv # Overview of code contributions +│ └── code_contributions_record.md # Overview of code contributions ├── src │ └── original # Original contributed code organized per contribution │ └── DS_BW_VanderBiltUMC_USA @@ -31,7 +31,8 @@ OSIPI/DCE-DSC-MRI_CodeCollection Wiki # Information and guidelines ``` -Click [here](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/blob/develop/doc/code_contributions_record.csv) for database of code available and testing status +Click [here](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/blob/develop/doc/code_contributions_record.md) for +database of code available and testing status The results of the validated code are published on the [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults). From d558c55e5fad079d5fca517b897e18b3cff94817 Mon Sep 17 00:00:00 2001 From: OSIPI Date: Thu, 3 Nov 2022 16:59:46 +0000 Subject: [PATCH 14/21] commit code_contributions_record.md --- doc/code_contributions_record.md | 89 ++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 doc/code_contributions_record.md diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md new file mode 100644 index 00000000..bc82170e --- /dev/null +++ b/doc/code_contributions_record.md @@ -0,0 +1,89 @@ +| Technique | Category | Subcategory (link) | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | +|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| +| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | 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 | nan | 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 | \ No newline at end of file From 65b0842e1e4b1d4162fc01f3615919c66fec6baf Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 17:01:12 +0000 Subject: [PATCH 15/21] update --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cc468afb..6c6fc4ef 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ OSIPI/DCE-DSC-MRI_CodeCollection Wiki # Information and guidelines ``` -Click [here](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/blob/develop/doc/code_contributions_record.md) for +Click [here](doc/code_contributions_record.md) for database of code available and testing status The results of the validated code are published on the [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults). From 510775b634d29cf22c3884bffea1d66c3d9ffa8d Mon Sep 17 00:00:00 2001 From: mjt320 Date: Thu, 3 Nov 2022 17:06:35 +0000 Subject: [PATCH 16/21] update --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 576db5a0..face8ba1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: git add doc/code_contributions_record.md git config --global user.name 'OSIPI' git config --global user.email 'OSIPI@users.noreply.github.com' - git commit -am "commit code_contributions_record.md" + git diff --exit-code || git commit -am "commit code_contributions_record.md" git push # build: From d24d2ea9b4c4d091413317be142fd6b105674115 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Tue, 8 Nov 2022 16:04:18 +0000 Subject: [PATCH 17/21] links added --- README.md | 7 +- doc/code_contributions_record.csv | 174 +++++++++++++++--------------- 2 files changed, 93 insertions(+), 88 deletions(-) diff --git a/README.md b/README.md index 6c6fc4ef..9b44cba6 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,11 @@ [![build Actions Status](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/workflows/ci/badge.svg)](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/actions) [![codecov](https://codecov.io/gh/OSIPI/DCE-DSC-MRI_CodeCollection/branch/develop/graph/badge.svg?token=ZR3RPV8Y0B)](https://codecov.io/gh/OSIPI/DCE-DSC-MRI_CodeCollection) + + +- [code database with links to source code](doc/code_contributions_record.md) +- [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults) + The ISMRM Open Science Initiative for Perfusion Imaging ([OSIPI](https://www.osipi.org/)) aims to promote the sharing of perfusion imaging software in order to reduce duplication, improve reproducibility and speed up translation. This **DCE-DSC-MRI_CodeCollection** code library is maintained by [Taskforce 2.3](https://www.osipi.org/task-force-2-3/) of OSIPI and aims to collect, test and share open-source perfusion imaging code for use in research and software development. Code contributions can include modules covering one or more steps within the image processing pipeline, for example T1 mapping, converting signal to concentration and pharmacokinetic modelling. A further aim of OSIPI is to develop a fully tested and harmonised code library, drawing on the contributions within this repository. A summary of the repository structure is shown below. More detailed information and documentation is located in the repository [wiki](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki) @@ -32,7 +37,7 @@ Wiki # Information and guidelines ``` Click [here](doc/code_contributions_record.md) for -database of code available and testing status +database of code available with links to code. The results of the validated code are published on the [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults). diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 1322848a..821978e4 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -1,88 +1,88 @@ -Technique,Category,Subcategory (link),Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) +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](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, -DCE,Bolus arrival time,fitting Kety (Tofts) model to first third of the curve,,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, -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, -DCE,Input Functions,Parker AIF,,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,,tbd, -DCE,Input Functions,Parker AIF,"Parker AIF, Parker-like AIF",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,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",,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,,tbd,completed -DCE,Input Functions,AIF parameterization,,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, -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,,tbd, -DCE,Input Functions,Parker AIF,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, -DCE,Input Functions,load AIF,from txt,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, -DCE,Input Functions,AIF parameterization,fit gamma-variate function,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, -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,,JK/PvH,completed -DCE,Input Functions,Parker AIF,,PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",ParkerAIF,,JK/PvH,completed -DCE,Input Functions,Parker AIF,,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,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,,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,,tbd, -DCE,Parameter derivation,iAUC,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, -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",,tdd, -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",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCXM,,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCUM,,MJT,completed -DCE,Pharmacokinetic models,AATH,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",AATH,,tbd, -DCE,Pharmacokinetic models,extended Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",ExtKety,,ST/OGC,completed -DCE,Pharmacokinetic models,Patlak,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Patlak,,MJT,completed -DCE,Pharmacokinetic models,Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Kety,,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, -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, -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, -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",,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",,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",,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",,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",,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",,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",,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",,MJT,completed -DCE,Pharmacokinetic models,Patlak,LLSQ fitting,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,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",,tbd, -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",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,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",,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,,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",,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",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,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",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, NOR","TM, fitToModelLLSQ",,ST/OGC,completed -DCE,Pharmacokinetic models,1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",OneCompartment,,tbd, -DCE,Pharmacokinetic models,dual-inlet 1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletOneCompartment,,tbd, -DCE,Pharmacokinetic models,dual-inlet ext Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletExtendedTofts,,tbd, -DCE,Pharmacokinetic models,dual-inlet high-flow 2-cmp Gadoxetate,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletconc_HF2CGM,,tbd, -DCE,Pharmacokinetic models,extended Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",ExtendedTofts,,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",Tofts,,ST/OGC,completed -DCE,Pharmacokinetic models,high flow 2-cmp Gadoxetate,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",,,tbd, -DCE,Pharmacokinetic models,Patlak,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",PatlakModel,,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",,tbd, -DCE,Signal to Concentration,SPGR or GE-EPI,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed -DCE,Signal to concentration,SPGR,"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,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",,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",,LK,completed -DCE,Signal to concentration,SPGR,"reverse R1->C also available",ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",signals2conc,,LK,completed -DCE,T1,VFA,nonlinear,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",fit_R1,,tbd, -DCE,T1,VFA,despot,McGill_VFA,Zaki Ahmed,"McGill University, Canada",despot,,MJT,completed -DCE,T1,VFA,novifast,McGill_VFA,Zaki Ahmed,"McGill University, Canada",novifast,,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,,MJT,in-progress -DCE,T1,VFA,linear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete -DCE,T1,VFA,nonlinear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete -DCE,T1,VFA,two flip angles,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, -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,,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,,MJT,competed -DCE,T1,VFA,linear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE,T1,VFA,nonlinear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed -DCE/DSC,Miscellaneous,calculate SNR,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, -DCE/DSC,Miscellaneous,calculate enhancement ratio,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, -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, -DSC,Leakage correction,BSW,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress -DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, -DSC,Signal to deltaR2*,single echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, -DSC,Signal to deltaR2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, -DSC,Signal to R2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file +DCE,Bolus arrival time,[fitting Kety (Tofts) model to first third of the curve](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, +DCE,Input Functions,[load AIF](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dce_aif.py),load from txt,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",read_AIF,https://doi.org/10.21105/joss.03523,tbd, +DCE,Input Functions,[Parker AIF](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dce_aif.py),,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](../src/original/MJT_UoEdinburgh_UK/aifs.py),constructed from time-concentration data,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",patientSpecific,,tbd, +DCE,Input Functions,[Parker AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),"Parker AIF, Parker-like AIF",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,JK/PvH,completed +DCE,Input Functions,[Manning AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),Manning et al (https://doi.org/10.1002/mrm.28833),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ManningFast, ManningSlow",,tbd,completed +DCE,Input Functions,[Heye AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Heye,,tbd,completed +DCE,Input Functions,[AIF parameterization](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),,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, +DCE,Input Functions,[Head-and-neck population AIF](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),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,,tbd, +DCE,Input Functions,[Parker AIF](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, +DCE,Input Functions,[load AIF](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/ArterialInputFunction.py),from txt,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, +DCE,Input Functions,[AIF parameterization](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/ArterialInputFunction.py),fit gamma-variate function,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, +DCE,Input Functions,[Georgiou AIF](../src/original/PvH_NKI_NL/AIF/PopulationAIF.py),Georgiou et al (DOI: 10.1002/mrm.27524),PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",GeorgiouAIF,,JK/PvH,completed +DCE,Input Functions,[Parker AIF](../src/original/PvH_NKI_NL/AIF/PopulationAIF.py),,PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",ParkerAIF,,JK/PvH,completed +DCE,Input Functions,[Parker AIF](../src/original/ST_USyd_AUS/InputFunctions.py),,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,JK/PvH,completed +DCE,Input Functions,[preclinical AIF](../src/original/ST_USyd_AUS/InputFunctions.py),McGrath et al (DOI: 10.1002/mrm.21959),ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",preclinicalAIF,,JK/PvH,completed +DCE,Miscellaneous,[enhancement detection](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),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,,tbd, +DCE,Parameter derivation,[iAUC](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tissue_concentration.py),,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","tofts_integral, fit_tofts_model",,tdd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","ext_tofts_integral, fit_tofts_model",,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/LCB_BNI_USA/dce.py),NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCXM,,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCUM,,MJT,completed +DCE,Pharmacokinetic models,[AATH](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",AATH,,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",ExtKety,,ST/OGC,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Patlak,,MJT,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Kety,,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/two_cxm_model.py),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](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/two_cfm_model.py),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, +DCE,Pharmacokinetic models,[active uptake and efflux (AUEM)](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/active_uptake_model.py),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, +DCE,Pharmacokinetic models,[dual-inlet general model](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dibem.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",dibem,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tofts_model.py),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](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),LLSQ fitting,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,MJT,completed +DCE,Pharmacokinetic models,[steady-state vp](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,[steady-state vp](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),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,,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, NOR","TM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,[1-cmp](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",OneCompartment,,tbd, +DCE,Pharmacokinetic models,[dual-inlet 1-cmp](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletOneCompartment,,tbd, +DCE,Pharmacokinetic models,[dual-inlet ext Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletExtendedTofts,,tbd, +DCE,Pharmacokinetic models,[dual-inlet high-flow 2-cmp Gadoxetate](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletconc_HF2CGM,,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",ExtendedTofts,,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",Tofts,,ST/OGC,completed +DCE,Pharmacokinetic models,[high flow 2-cmp Gadoxetate](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",,,tbd, +DCE,Pharmacokinetic models,[Patlak](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",PatlakModel,,MJT,completed +DCE,Signal to Concentration,[SPGR](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),"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",,tbd, +DCE,Signal to Concentration,[SPGR or GE-EPI](../src/original/LCB_BNI_USA/dce.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/LEK_UoEdinburgh_UK/SignalToConcentration/SI2Conc.py),"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tissue_concentration.py),"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](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),"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",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),"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",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/ST_USyd_AUS/signals2conc.py),"reverse R1->C also available",ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",signals2conc,,LK,completed +DCE,T1,[VFA](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),nonlinear,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",fit_R1,,tbd, +DCE,T1,[VFA](../src/original/ZA_McGill_CAN/vfa.py),despot,McGill_VFA,Zaki Ahmed,"McGill University, Canada",despot,,MJT,completed +DCE,T1,[VFA](../src/original/ZA_McGill_CAN/vfa.py),novifast,McGill_VFA,Zaki Ahmed,"McGill University, Canada",novifast,,MJT,completed +DCE,T1,[DESPOT1-HIFI](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),Fit any combination of (IR-)SPGR scans to estimate T1,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",HIFI,,MJT,in-progress +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),linear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),nonlinear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),two flip angles,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, +DCE,T1,[VFA](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),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,,MJT,competed +DCE,T1,[VFA](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed +DCE,T1,[VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py),linear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE,T1,[VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py),nonlinear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE/DSC,AIF deconvolution,[Volterra discretization with L-curve criterion](../src/original/SR_TBG_BNIPhoenix_USA/AIFDeconvolution/AIF_deconvolution.py),,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed +DCE/DSC,Miscellaneous,[calculate SNR](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, +DCE/DSC,Miscellaneous,[calculate enhancement ratio](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, +DSC,Input Functions,[automatic AIF selection](../src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/AIF_selection_automatic.py),"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, +DSC,Leakage correction,[BSW](../src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/bsw_leakagecorr.py),,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress +DSC,Parameter derivation,"[CBV,CBF,MTT](../src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/DSC_parameters.py)",,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, +DSC,Signal to deltaR2*,[single echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, +DSC,Signal to deltaR2*,[dual echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, +DSC,Signal to R2*,[dual echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file From 9f4c43dd06d9cfb1b87780f4289bd0dce47cf7ee Mon Sep 17 00:00:00 2001 From: mjt320 Date: Tue, 8 Nov 2022 16:05:42 +0000 Subject: [PATCH 18/21] Add build task back into actions --- .github/workflows/ci.yml | 52 ++++++++++++++++++++-------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index face8ba1..f363e34a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,7 +9,7 @@ on: jobs: - convert: + convert csv to md: runs-on: ${{ matrix.os }} strategy: matrix: @@ -37,28 +37,28 @@ jobs: git diff --exit-code || git commit -am "commit code_contributions_record.md" git push -# build: -# -# runs-on: ${{ matrix.os }} -# strategy: -# matrix: -# os: [ubuntu-latest, macos-latest, windows-latest] -# python-version: [3.8] -# -# steps: -# - uses: actions/checkout@v2 -# - name: Set up Python ${{ matrix.python-version }} -# uses: actions/setup-python@v2 -# with: -# python-version: ${{ matrix.python-version }} -# - name: Install dependencies -# run: | -# python -m pip install --upgrade pip -# pip install wheel flake8 pytest codecov -# pip install ".[test]" -# - name: Test with pytest -# run: | -# coverage run -m pytest -# - name: Upload coverage to codecov -# run: | -# codecov + build: + + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + python-version: [3.8] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install wheel flake8 pytest codecov + pip install ".[test]" + - name: Test with pytest + run: | + coverage run -m pytest + - name: Upload coverage to codecov + run: | + codecov From 4540914e2d4d59bc37d751df516c51e55580e6a0 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Tue, 8 Nov 2022 16:07:10 +0000 Subject: [PATCH 19/21] correct job name --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f363e34a..9daa2aa9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,7 +9,7 @@ on: jobs: - convert csv to md: + convert_csv_to_md: runs-on: ${{ matrix.os }} strategy: matrix: From 9877e68867fc9a04775b1b83895ca07eddd0d0a2 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Tue, 8 Nov 2022 16:24:56 +0000 Subject: [PATCH 20/21] add jupyterbook workflow back in --- .github/workflows/jupyterbook.yml | 94 +++++++++++++++---------------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/.github/workflows/jupyterbook.yml b/.github/workflows/jupyterbook.yml index b563067e..1a4007d8 100644 --- a/.github/workflows/jupyterbook.yml +++ b/.github/workflows/jupyterbook.yml @@ -7,50 +7,50 @@ on: - develop # This job installs dependencies, build the book, and pushes it to `gh-pages` -#jobs: -# build-and-deploy-book: -# runs-on: ${{ matrix.os }} -# strategy: -# matrix: -# os: [ubuntu-latest] -# python-version: [3.8] -# steps: -# - uses: actions/checkout@v2 -# -# # Install dependencies -# - name: Set up Python ${{ matrix.python-version }} -# uses: actions/setup-python@v1 -# with: -# python-version: ${{ matrix.python-version }} -# - name: Install dependencies -# run: | -# pip install wheel pytest -# pip install -r notebooks/requirements.txt -# pip install . -# -# - name: Test with pytest -# run: | -# pytest . -# -# # Build the book -# - name: Build the book -# run: | -# jupyter-book build notebooks/ -# touch notebooks/_build/html/.nojekyll -# -# - name: Re-organize files -# run: | -# mkdir out -# mv notebooks/_build/html out/docs -# mv test out/test -# -# # Deploy the book's HTML to another repo -# - name: publish:starters -# uses: cpina/github-action-push-to-another-repository@master -# env: -# API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }} -# with: -# source-directory: 'out' -# destination-github-username: 'OSIPI' -# destination-repository-name: 'DCE-DSC-MRI_TestResults' -# user-email: zaki@live.ca \ No newline at end of file +jobs: + build-and-deploy-book: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + python-version: [3.8] + steps: + - uses: actions/checkout@v2 + + # Install dependencies + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + pip install wheel pytest + pip install -r notebooks/requirements.txt + pip install . + + - name: Test with pytest + run: | + pytest . + + # Build the book + - name: Build the book + run: | + jupyter-book build notebooks/ + touch notebooks/_build/html/.nojekyll + + - name: Re-organize files + run: | + mkdir out + mv notebooks/_build/html out/docs + mv test out/test + + # Deploy the book's HTML to another repo + - name: publish:starters + uses: cpina/github-action-push-to-another-repository@master + env: + API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }} + with: + source-directory: 'out' + destination-github-username: 'OSIPI' + destination-repository-name: 'DCE-DSC-MRI_TestResults' + user-email: zaki@live.ca \ No newline at end of file From d95b99fe9b7a6a4640838107dcd403fa160daaef Mon Sep 17 00:00:00 2001 From: mjt320 Date: Tue, 8 Nov 2022 16:36:00 +0000 Subject: [PATCH 21/21] separate workflows --- .github/workflows/ci.yml | 28 ----------------------- .github/workflows/convert_csv.yml | 37 +++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+), 28 deletions(-) create mode 100644 .github/workflows/convert_csv.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9daa2aa9..06c22a58 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,34 +9,6 @@ on: jobs: - convert_csv_to_md: - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest] - python-version: [3.8] - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - pip install wheel pandas - pip install wheel tabulate - - name: Run script to convert table - run: | - python doc/convert_to_md.py - - name: Commit md file - run: | - git add doc/code_contributions_record.md - git config --global user.name 'OSIPI' - git config --global user.email 'OSIPI@users.noreply.github.com' - git diff --exit-code || git commit -am "commit code_contributions_record.md" - git push - build: runs-on: ${{ matrix.os }} diff --git a/.github/workflows/convert_csv.yml b/.github/workflows/convert_csv.yml new file mode 100644 index 00000000..844a2e50 --- /dev/null +++ b/.github/workflows/convert_csv.yml @@ -0,0 +1,37 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: convert_csv + +on: + - push + +jobs: + + convert_csv_to_md: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + python-version: [3.8] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + pip install wheel pandas + pip install wheel tabulate + - name: Run script to convert table + run: | + python doc/convert_to_md.py + - name: Commit md file + run: | + git add doc/code_contributions_record.md + git config --global user.name 'OSIPI' + git config --global user.email 'OSIPI@users.noreply.github.com' + git diff --exit-code || git commit -am "commit code_contributions_record.md" + git push