diff --git a/.github/workflows/convert_csv.yml b/.github/workflows/convert_csv.yml deleted file mode 100644 index 1f0d5c96..00000000 --- a/.github/workflows/convert_csv.yml +++ /dev/null @@ -1,40 +0,0 @@ -# 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 doc/code_contributions_record.md" -# git push - - uses: stefanzweifel/git-auto-commit-action@v4 - with: - commit_message: commit doc/code_contributions_record.md diff --git a/.github/workflows/jupyterbook.yml b/.github/workflows/jupyterbook.yml index 1a4007d8..fc6642f8 100644 --- a/.github/workflows/jupyterbook.yml +++ b/.github/workflows/jupyterbook.yml @@ -27,17 +27,17 @@ jobs: pip install wheel pytest pip install -r notebooks/requirements.txt pip install . - - name: Test with pytest run: | pytest . - # Build the book + - name: Convert contributors csv to md + run: | + python doc/convert_to_md.py - name: Build the book run: | jupyter-book build notebooks/ touch notebooks/_build/html/.nojekyll - - name: Re-organize files run: | mkdir out diff --git a/README.md b/README.md index 9b44cba6..f56b7933 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ -- [code database with links to source code](doc/code_contributions_record.md) -- [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults) +- [code database with links to source code](https://osipi.org/DCE-DSC-MRI_TestResults/overview_of_code_collection.html) +- [test-results website](https://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. @@ -43,4 +43,4 @@ The results of the validated code are published on the [test-results website](ht -This is an ongoing project, we welcome new contributions. If you would like to contribute to the OSIPI initiative please email the contacts listed on our [website](https://www.osipi.org/task-force-2-3/). \ No newline at end of file +This is an ongoing project, we welcome new contributions. If you would like to contribute to the OSIPI initiative please email the contacts listed on our [website](https://www.osipi.org/task-force-2-3/). diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md deleted file mode 100644 index dc8e904f..00000000 --- a/doc/code_contributions_record.md +++ /dev/null @@ -1,89 +0,0 @@ -| 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 | nan | tbd | nan | -| DCE | Bolus arrival time | [fitting Kety (Tofts) model to first third of the curve](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | nan | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | BAT_kety | nan | tbd | nan | -| 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 | nan | -| DCE | Input Functions | [Parker AIF](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dce_aif.py) | 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](../src/original/MJT_UoEdinburgh_UK/aifs.py) | constructed from time-concentration data | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | patientSpecific | nan | tbd | nan | -| 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 | nan | 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 | nan | 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 | nan | tbd | completed | -| DCE | Input Functions | [AIF parameterization](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py) | 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](../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 | nan | tbd | nan | -| DCE | Input Functions | [Parker AIF](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py) | 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](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/ArterialInputFunction.py) | from txt | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | loadStandard | nan | tbd | nan | -| 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 | nan | tbd | nan | -| 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 | nan | JK/PvH | completed | -| DCE | Input Functions | [Parker AIF](../src/original/PvH_NKI_NL/AIF/PopulationAIF.py) | nan | PvH_NKI | Petra van Houdt | the Netherlands Cancer Institute, the Netherlands | ParkerAIF | nan | JK/PvH | completed | -| DCE | Input Functions | [Parker AIF](../src/original/ST_USyd_AUS/InputFunctions.py) | nan | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | AIF, variableAIF | nan | 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 | nan | 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 | nan | tbd | nan | -| DCE | Parameter derivation | [iAUC](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tissue_concentration.py) | 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](../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 | nan | tdd | nan | -| 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 | nan | tbd | nan | -| 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 | nan | 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 | nan | 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 | nan | 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 | nan | tbd | nan | -| DCE | Pharmacokinetic models | [extended Tofts](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py) | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | ExtKety | nan | 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 | nan | 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 | nan | 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 | nan | -| 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 | nan | -| 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 | nan | -| 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | tbd | nan | -| 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 | nan | tbd | nan | -| 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | tbd | nan | -| 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 | nan | tbd | nan | -| 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 | nan | tbd | nan | -| 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 | nan | tbd | nan | -| DCE | Pharmacokinetic models | [extended Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py) | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | ExtendedTofts | nan | 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 | nan | 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 | nan | nan | tbd | nan | -| DCE | Pharmacokinetic models | [Patlak](../src/original/ST_USyd_AUS/ModelDictionary.py) | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | PatlakModel | nan | 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 | nan | tbd | nan | -| DCE | Signal to Concentration | [SPGR or GE-EPI](../src/original/LCB_BNI_USA/dce.py) | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | signal_to_conc, estimate_delta_R1 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | 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 | nan | tbd | nan | -| DCE | T1 | [VFA](../src/original/ZA_McGill_CAN/vfa.py) | despot | McGill_VFA | Zaki Ahmed | McGill University, Canada | despot | nan | MJT | completed | -| DCE | T1 | [VFA](../src/original/ZA_McGill_CAN/vfa.py) | novifast | McGill_VFA | Zaki Ahmed | McGill University, Canada | novifast | nan | 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 | nan | 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 | nan | MJT | complete | -| DCE | T1 | [VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py) | nonlinear | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | VFANonlinear | nan | 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 | nan | tbd | nan | -| 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 | nan | 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 | nan | MJT | competed | -| DCE | T1 | [VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py) | linear | ST_Sydney_AUS_T1 | Sirisha Tadimalla | University of Sydney, Australia | VFAT1mapping | nan | MJT | completed | -| DCE | T1 | [VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py) | nonlinear | ST_Sydney_AUS_T1 | Sirisha Tadimalla | University of Sydney, Australia | VFAT1mapping | nan | MJT | completed | -| DCE/DSC | AIF deconvolution | [Volterra discretization with L-curve criterion](../src/original/SR_TBG_BNIPhoenix_USA/AIFDeconvolution/AIF_deconvolution.py) | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | AIFdeconvolution | nan | JA | completed | -| DCE/DSC | Miscellaneous | [calculate SNR](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py) | 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](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py) | 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](../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 | nan | -| DSC | Leakage correction | [BSW](../src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/bsw_leakagecorr.py) | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | BSWleakagecorr | nan | SR | in-progress | -| DSC | Parameter derivation | [CBV,CBF,MTT](../src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/DSC_parameters.py) | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | DSCparameters | nan | tbd | nan | -| DSC | Signal to deltaR2* | [single echo](../src/original/LCB_BNI_USA/dsc.py) | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_delta_R2s | tbd | nan | -| DSC | Signal to deltaR2* | [dual echo](../src/original/LCB_BNI_USA/dsc.py) | 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](../src/original/LCB_BNI_USA/dsc.py) | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_R2s | tbd | nan | \ No newline at end of file diff --git a/doc/convert_to_md.py b/doc/convert_to_md.py index 93d53261..c7875df1 100644 --- a/doc/convert_to_md.py +++ b/doc/convert_to_md.py @@ -1,5 +1,7 @@ import pandas as pd 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 +md = df.to_markdown(index=False).replace("(../", "(https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/tree/develop/") +with open('notebooks/overview_of_code_collection.md', 'w') as f: + f.write("# Overview of code collection\n\n") + f.write(md) diff --git a/notebooks/_toc.yml b/notebooks/_toc.yml index d618c4c3..5d05de42 100644 --- a/notebooks/_toc.yml +++ b/notebooks/_toc.yml @@ -4,7 +4,7 @@ format: jb-article root: intro.md sections: -- file: contributors.ipynb +- file: overview_of_code_collection.md - file: DCE.md sections: - file: T1mapping.md diff --git a/notebooks/contributors.ipynb b/notebooks/contributors.ipynb deleted file mode 100644 index c6f77a34..00000000 --- a/notebooks/contributors.ipynb +++ /dev/null @@ -1,1549 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Overview of code collection" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "This is a table of current code contributions." - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "tags": [ - "remove-input" - ] - }, - "outputs": [], - "source": [ - "import pandas as pd" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "tags": [ - "remove-input" - ] - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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TechniqueCategorySubcategoryNotesSubfolderAuthorsInstitutionTesterTest status (empty/in-progress/complete)Unnamed: 9
0DCEBolus arrival timepiecewise linear quadratic functionCheong et al (DOI: 10.1088/0031-9155/48/5/403)LEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdNaNNaN
1DCEBolus arrival timefitting Kety (Tofts) model to first third of t...NaNLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdNaNNaN
2DCEConcentration to enhancementNaNNaNMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdin-progressNaN
3DCEConcentration to R1NaNNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdin-progressNaN
4DCEConcentration to signalSPGRNaNLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdNaNNaN
5DCEConcentration to signalSPGRNaNMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKtbdNaNNaN
6DCEConcentration to signalSPGRNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdNaNNaN
7DCEInput FunctionsAIF parameterizationNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdNaNNaN
8DCEInput FunctionsGeorgiou AIFGeorgiou et al (DOI: 10.1002/mrm.27524)PvH_NKIPetra van Houdtthe Netherlands Cancer Institute, the NetherlandsJK/PvHin-progressNaN
9DCEInput FunctionsHead-and-neck population AIFWong et al (DOI: https://doi.org/10.2967/jnume...OG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...JK/PvHin-progressNaN
10DCEInput Functionsload AIFload from txtMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKtbdNaNNaN
11DCEInput Functionsload AIFfrom txt, gamma-variate functionOGJ_OsloU_NorwayOle Gunnar JohansenUniversity of Oslo, NorwaytbdNaNNaN
12DCEInput FunctionsParker AIFNaNST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliaJK/PvHin-progressNaN
13DCEInput FunctionsParker AIFNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...JK/PvHin-progressNaN
14DCEInput FunctionsParker AIFNaNPvH_NKIPetra van Houdtthe Netherlands Cancer Institute, the NetherlandsJK/PvHin-progressNaN
15DCEInput FunctionsParker AIFParker AIF, Parker-like AIFMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKJK/PvHin-progressNaN
16DCEInput FunctionsParker AIFNaNMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKJK/PvHin-progressNaN
17DCEInput Functionspatient-specific AIFmeasured AIFMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdNaNNaN
18DCEInput Functionspreclinical AIFMcGrath et al (DOI: 10.1002/mrm.21959)ST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliaJK/PvHin-progressNaN
19DCEParameter derivationiAUCNaNMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKtbdNaNNaN
20DCEPharmacokinetic models1-cmpforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
21DCEPharmacokinetic models2-cmp exchangeforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdin-progressNaN
22DCEPharmacokinetic models2-cmp exchangeforward model, NLLS and LLSQ fitting methodsOGJ_OsloU_NorwayOle Gunnar JohansenUniversity of Oslo, Norwaytbdin-progressNaN
23DCEPharmacokinetic models2-cmp exchangeforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdin-progressNaN
24DCEPharmacokinetic models2-cmp exchangeforward model, LLSQ fitting methodsMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKST/OGCin-progressNaN
25DCEPharmacokinetic models2-cmp filtrationforward model, LLSQ fitting methodsMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKST/OGCin-progressNaN
26DCEPharmacokinetic models2-cmp uptakeforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdin-progressNaN
27DCEPharmacokinetic models2-cmp uptakeforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdin-progressNaN
28DCEPharmacokinetic modelsAATHforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdin-progressNaN
29DCEPharmacokinetic modelsactive uptake and efflux (AUEM)forward model, LLSQ fitting methodsMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKST/OGCin-progressNaN
30DCEPharmacokinetic modelsdual-inlet 1-cmpforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
31DCEPharmacokinetic modelsdual-inlet ext Toftsforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
32DCEPharmacokinetic modelsdual-inlet general modelworks with 2CXM, 2CFM, AUEM, LLSQ fitting methodsMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKST/OGCin-progressNaN
33DCEPharmacokinetic modelsdual-inlet high-flow 2-cmp Gadoxetateforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
34DCEPharmacokinetic modelsextended Toftsforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKST/OGCin-progressNaN
35DCEPharmacokinetic modelsextended Toftsforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliaST/OGCin-progressNaN
36DCEPharmacokinetic modelsextended Toftsforward model, NLLS fitting methodsOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...ST/OGCin-progressNaN
37DCEPharmacokinetic modelsextended Toftsforward model, NLLS and LLSQ fitting methodsOGJ_OsloU_NorwayOle Gunnar JohansenUniversity of Oslo, NorwayST/OGCin-progressNaN
38DCEPharmacokinetic modelsextended Toftsforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKST/OGCin-progressNaN
39DCEPharmacokinetic modelsextended Toftsforward model, LLSQ fitting methodsMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKST/OGCin-progressNaN
40DCEPharmacokinetic modelshigh flow 2-cmp Gadoxetateforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
41DCEPharmacokinetic modelsPatlakforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKtbdin-progressNaN
42DCEPharmacokinetic modelsPatlakforward modelST_USydAUS_DCESirisha TadimallaUniversity of Sydney, Australiatbdin-progressNaN
43DCEPharmacokinetic modelsPatlakforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdin-progressNaN
44DCEPharmacokinetic modelssteady-state vpforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdin-progressNaN
45DCEPharmacokinetic modelsToftsforward modelLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKST/OGCin-progressNaN
46DCEPharmacokinetic modelsToftsforward model, NLLS and LLSQ fitting methodsOGJ_OsloU_NorwayOle Gunnar JohansenUniversity of Oslo, NorwayST/OGCin-progressNaN
47DCEPharmacokinetic modelsToftsforward model, NLLS fitting (concentration), N...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKST/OGCin-progressNaN
48DCEPharmacokinetic modelsToftsforward model, NLLS fitting methodsLCB_BNI_USALaura BellBarrow Neurological Institute, USAST/OGCin-progressNaN
49DCEPreprocessingenhancement detectioncheck for enhancementOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdNaNNaN
50DCER1 to concentrationNaNNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdin-progressNaN
51DCER1 to signalSPGRNaNST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliatbdNaNNaN
52DCER1 to signalSPGRNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdNaNNaN
53DCESignal to concentrationSPGRNaNLEK_UoEdinburghLucy KershawUniversity of Edinburgh, UKLKcompletedNaN
54DCESignal to concentrationSPGRNaNST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliaLKcompletedNaN
55DCESignal to concentrationSPGRNaNMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKLKcompletedNaN
56DCESignal to concentrationSPGRNaNMB_QBI_UoManchester_UKMichael BerksUniversity of Manchester, UKLKcompletedNaN
57DCESignal to concentrationSPGR or GE-EPINaNLCB_BNI_USALaura BellBarrow Neurological Institute, USALKcompletedNaN
58DCESignal to enhancementNaNNaNMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKtbdNaNNaN
59DCESignal to R1SPGRNaNST_USydAUS_DCESirisha TadimallaUniversity of Sydney, AustraliatbdNaNNaN
60DCESignal to R1SPGRNaNOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...tbdNaNNaN
61DCESignal to R1SPGR or GE-EPINaNLCB_BNI_USALaura BellBarrow Neurological Institute, USAtbdNaNNaN
62DCET1DESPOT1-HIFIFit any combination of (IR-)SPGR scans to esti...MJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKMJTin-progressNaN
63DCET1VFAlinear, nonlinearST_Sydney_AUS_T1Sirisha TadimallaUniversity of Sydney, AustraliaMJTcompleteNaN
64DCET1VFAlinear, nonlinear, two flip anglesMJT_UoEdinburgh_UKMichael ThrippletonUniversity of Edinburgh, UKMJTcompleteNaN
65DCET1VFAtwo flip anglesOG_MO_AUMC_ICR_RMHOliver Gurney-Champion, Matthew OrtonAmsterdam University Medical Center, the Nethe...MJTin-progressNaN
66DCET1VFAdespot, novifastMcGill_VFAZaki AhmedMcGill University, CanadaMJTcompleteNaN
67DCE/DSCAIF deconvolutionNaNNaNSR_TBG_BNI_PhoenixUSASudarshan RagunathanBarrow Neurological Institute, USAtbdNaNNaN
68DSCInput Functionsautomatic AIF selectionfully automatic, semi-automaticJBJA_GUSahlgrenskaSWEJesper Browall, Jonathan ArvidssonSahlgrenska University Hospital and Gothenburg...tbdNaNNaN
69DSCLeakage correctionBSWNaNSR_TBG_BNI_PhoenixUSASudarshan RagunathanBarrow Neurological Institute, USAtbdNaNNaN
70DSCLeakage correctionBSWNaNLCB_BNI_USALaura BellBarrow Neurological Institute, USAtbdNaNNaN
71DSCParameter derivationCBV,CBF,MTTNaNLCB_BNI_USALaura BellBarrow Neurological Institute, USAtbdNaNNaN
72DSCParameter derivationCBV,CBF,MTTNaNSR_TBG_BNI_PhoenixUSASudarshan RagunathanBarrow Neurological Institute, USAtbdNaNNaN
73DSCSignal to deltaR2*single echo, dual echoNaNLCB_BNI_USALaura BellBarrow Neurological Institute, USAtbdNaNNaN
74DSCSignal to R2*dual echoNaNLCB_BNI_USALaura BellBarrow Neurological Institute, USAtbdNaNNaN
\n", - "
" - ], - "text/plain": [ - " Technique Category \\\n", - "0 DCE Bolus arrival time \n", - "1 DCE Bolus arrival time \n", - "2 DCE Concentration to enhancement \n", - "3 DCE Concentration to R1 \n", - "4 DCE Concentration to signal \n", - "5 DCE Concentration to signal \n", - "6 DCE Concentration to signal \n", - "7 DCE Input Functions \n", - "8 DCE Input Functions \n", - "9 DCE Input Functions \n", - "10 DCE Input Functions \n", - "11 DCE Input Functions \n", - "12 DCE Input Functions \n", - "13 DCE Input Functions \n", - "14 DCE Input Functions \n", - "15 DCE Input Functions \n", - "16 DCE Input Functions \n", - "17 DCE Input Functions \n", - "18 DCE Input Functions \n", - "19 DCE Parameter derivation \n", - "20 DCE Pharmacokinetic models \n", - "21 DCE Pharmacokinetic models \n", - "22 DCE Pharmacokinetic models \n", - "23 DCE Pharmacokinetic models \n", - "24 DCE Pharmacokinetic models \n", - "25 DCE Pharmacokinetic models \n", - "26 DCE Pharmacokinetic models \n", - "27 DCE Pharmacokinetic models \n", - "28 DCE Pharmacokinetic models \n", - "29 DCE Pharmacokinetic models \n", - "30 DCE Pharmacokinetic models \n", - "31 DCE Pharmacokinetic models \n", - "32 DCE Pharmacokinetic models \n", - "33 DCE Pharmacokinetic models \n", - "34 DCE Pharmacokinetic models \n", - "35 DCE Pharmacokinetic models \n", - "36 DCE Pharmacokinetic models \n", - "37 DCE Pharmacokinetic models \n", - "38 DCE Pharmacokinetic models \n", - "39 DCE Pharmacokinetic models \n", - "40 DCE Pharmacokinetic models \n", - "41 DCE Pharmacokinetic models \n", - "42 DCE Pharmacokinetic models \n", - "43 DCE Pharmacokinetic models \n", - "44 DCE Pharmacokinetic models \n", - "45 DCE Pharmacokinetic models \n", - "46 DCE Pharmacokinetic models \n", - "47 DCE Pharmacokinetic models \n", - "48 DCE Pharmacokinetic models \n", - "49 DCE Preprocessing \n", - "50 DCE R1 to concentration \n", - "51 DCE R1 to signal \n", - "52 DCE R1 to signal \n", - "53 DCE Signal to concentration \n", - "54 DCE Signal to concentration \n", - "55 DCE Signal to concentration \n", - "56 DCE Signal to concentration \n", - "57 DCE Signal to concentration \n", - "58 DCE Signal to enhancement \n", - "59 DCE Signal to R1 \n", - "60 DCE Signal to R1 \n", - "61 DCE Signal to R1 \n", - "62 DCE T1 \n", - "63 DCE T1 \n", - "64 DCE T1 \n", - "65 DCE T1 \n", - "66 DCE T1 \n", - "67 DCE/DSC AIF deconvolution \n", - "68 DSC Input Functions \n", - "69 DSC Leakage correction \n", - "70 DSC Leakage correction \n", - "71 DSC Parameter derivation \n", - "72 DSC Parameter derivation \n", - "73 DSC Signal to deltaR2* \n", - "74 DSC Signal to R2* \n", - "\n", - " Subcategory \\\n", - "0 piecewise linear quadratic function \n", - "1 fitting Kety (Tofts) model to first third of t... \n", - "2 NaN \n", - "3 NaN \n", - "4 SPGR \n", - "5 SPGR \n", - "6 SPGR \n", - "7 AIF parameterization \n", - "8 Georgiou AIF \n", - "9 Head-and-neck population AIF \n", - "10 load AIF \n", - "11 load AIF \n", - "12 Parker AIF \n", - "13 Parker AIF \n", - "14 Parker AIF \n", - "15 Parker AIF \n", - "16 Parker AIF \n", - "17 patient-specific AIF \n", - "18 preclinical AIF \n", - "19 iAUC \n", - "20 1-cmp \n", - "21 2-cmp exchange \n", - "22 2-cmp exchange \n", - "23 2-cmp exchange \n", - "24 2-cmp exchange \n", - "25 2-cmp filtration \n", - "26 2-cmp uptake \n", - "27 2-cmp uptake \n", - "28 AATH \n", - "29 active uptake and efflux (AUEM) \n", - "30 dual-inlet 1-cmp \n", - "31 dual-inlet ext Tofts \n", - "32 dual-inlet general model \n", - "33 dual-inlet high-flow 2-cmp Gadoxetate \n", - "34 extended Tofts \n", - "35 extended Tofts \n", - "36 extended Tofts \n", - "37 extended Tofts \n", - "38 extended Tofts \n", - "39 extended Tofts \n", - "40 high flow 2-cmp Gadoxetate \n", - "41 Patlak \n", - "42 Patlak \n", - "43 Patlak \n", - "44 steady-state vp \n", - "45 Tofts \n", - "46 Tofts \n", - "47 Tofts \n", - "48 Tofts \n", - "49 enhancement detection \n", - "50 NaN \n", - "51 SPGR \n", - "52 SPGR \n", - "53 SPGR \n", - "54 SPGR \n", - "55 SPGR \n", - "56 SPGR \n", - "57 SPGR or GE-EPI \n", - "58 NaN \n", - "59 SPGR \n", - "60 SPGR \n", - "61 SPGR or GE-EPI \n", - "62 DESPOT1-HIFI \n", - "63 VFA \n", - "64 VFA \n", - "65 VFA \n", - "66 VFA \n", - "67 NaN \n", - "68 automatic AIF selection \n", - "69 BSW \n", - "70 BSW \n", - "71 CBV,CBF,MTT \n", - "72 CBV,CBF,MTT \n", - "73 single echo, dual echo \n", - "74 dual echo \n", - "\n", - " Notes Subfolder \\\n", - "0 Cheong et al (DOI: 10.1088/0031-9155/48/5/403) LEK_UoEdinburgh \n", - "1 NaN LEK_UoEdinburgh \n", - "2 NaN MJT_UoEdinburgh_UK \n", - "3 NaN OG_MO_AUMC_ICR_RMH \n", - "4 NaN LEK_UoEdinburgh \n", - "5 NaN MB_QBI_UoManchester_UK \n", - "6 NaN OG_MO_AUMC_ICR_RMH \n", - "7 NaN OG_MO_AUMC_ICR_RMH \n", - "8 Georgiou et al (DOI: 10.1002/mrm.27524) PvH_NKI \n", - "9 Wong et al (DOI: https://doi.org/10.2967/jnume... OG_MO_AUMC_ICR_RMH \n", - "10 load from txt MB_QBI_UoManchester_UK \n", - "11 from txt, gamma-variate function OGJ_OsloU_Norway \n", - "12 NaN ST_USydAUS_DCE \n", - "13 NaN OG_MO_AUMC_ICR_RMH \n", - "14 NaN PvH_NKI \n", - "15 Parker AIF, Parker-like AIF MJT_UoEdinburgh_UK \n", - "16 NaN MB_QBI_UoManchester_UK \n", - "17 measured AIF MJT_UoEdinburgh_UK \n", - "18 McGrath et al (DOI: 10.1002/mrm.21959) ST_USydAUS_DCE \n", - "19 NaN MB_QBI_UoManchester_UK \n", - "20 forward model ST_USydAUS_DCE \n", - "21 forward model LEK_UoEdinburgh \n", - "22 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "23 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "24 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", - "25 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", - "26 forward model LEK_UoEdinburgh \n", - "27 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "28 forward model LEK_UoEdinburgh \n", - "29 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", - "30 forward model ST_USydAUS_DCE \n", - "31 forward model ST_USydAUS_DCE \n", - "32 works with 2CXM, 2CFM, AUEM, LLSQ fitting methods MB_QBI_UoManchester_UK \n", - "33 forward model ST_USydAUS_DCE \n", - "34 forward model LEK_UoEdinburgh \n", - "35 forward model ST_USydAUS_DCE \n", - "36 forward model, NLLS fitting methods OG_MO_AUMC_ICR_RMH \n", - "37 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "38 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "39 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", - "40 forward model ST_USydAUS_DCE \n", - "41 forward model LEK_UoEdinburgh \n", - "42 forward model ST_USydAUS_DCE \n", - "43 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "44 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "45 forward model LEK_UoEdinburgh \n", - "46 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "47 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", - "48 forward model, NLLS fitting methods LCB_BNI_USA \n", - "49 check for enhancement OG_MO_AUMC_ICR_RMH \n", - "50 NaN OG_MO_AUMC_ICR_RMH \n", - "51 NaN ST_USydAUS_DCE \n", - "52 NaN OG_MO_AUMC_ICR_RMH \n", - "53 NaN LEK_UoEdinburgh \n", - "54 NaN ST_USydAUS_DCE \n", - "55 NaN MJT_UoEdinburgh_UK \n", - "56 NaN MB_QBI_UoManchester_UK \n", - "57 NaN LCB_BNI_USA \n", - "58 NaN MJT_UoEdinburgh_UK \n", - "59 NaN ST_USydAUS_DCE \n", - "60 NaN OG_MO_AUMC_ICR_RMH \n", - "61 NaN LCB_BNI_USA \n", - "62 Fit any combination of (IR-)SPGR scans to esti... MJT_UoEdinburgh_UK \n", - "63 linear, nonlinear ST_Sydney_AUS_T1 \n", - "64 linear, nonlinear, two flip angles MJT_UoEdinburgh_UK \n", - "65 two flip angles OG_MO_AUMC_ICR_RMH \n", - "66 despot, novifast McGill_VFA \n", - "67 NaN SR_TBG_BNI_PhoenixUSA \n", - "68 fully automatic, semi-automatic JBJA_GUSahlgrenskaSWE \n", - "69 NaN SR_TBG_BNI_PhoenixUSA \n", - "70 NaN LCB_BNI_USA \n", - "71 NaN LCB_BNI_USA \n", - "72 NaN SR_TBG_BNI_PhoenixUSA \n", - "73 NaN LCB_BNI_USA \n", - "74 NaN LCB_BNI_USA \n", - "\n", - " Authors \\\n", - "0 Lucy Kershaw \n", - "1 Lucy Kershaw \n", - "2 Michael Thrippleton \n", - "3 Oliver Gurney-Champion, Matthew Orton \n", - "4 Lucy Kershaw \n", - "5 Michael Berks \n", - "6 Oliver Gurney-Champion, Matthew Orton \n", - "7 Oliver Gurney-Champion, Matthew Orton \n", - "8 Petra van Houdt \n", - "9 Oliver Gurney-Champion, Matthew Orton \n", - "10 Michael Berks \n", - "11 Ole Gunnar Johansen \n", - "12 Sirisha Tadimalla \n", - "13 Oliver Gurney-Champion, Matthew Orton \n", - "14 Petra van Houdt \n", - "15 Michael Thrippleton \n", - "16 Michael Berks \n", - "17 Michael Thrippleton \n", - "18 Sirisha Tadimalla \n", - "19 Michael Berks \n", - "20 Sirisha Tadimalla \n", - "21 Lucy Kershaw \n", - "22 Ole Gunnar Johansen \n", - "23 Michael Thrippleton \n", - "24 Michael Berks \n", - "25 Michael Berks \n", - "26 Lucy Kershaw \n", - "27 Michael Thrippleton \n", - "28 Lucy Kershaw \n", - "29 Michael Berks \n", - "30 Sirisha Tadimalla \n", - "31 Sirisha Tadimalla \n", - "32 Michael Berks \n", - "33 Sirisha Tadimalla \n", - "34 Lucy Kershaw \n", - "35 Sirisha Tadimalla \n", - "36 Oliver Gurney-Champion, Matthew Orton \n", - "37 Ole Gunnar Johansen \n", - "38 Michael Thrippleton \n", - "39 Michael Berks \n", - "40 Sirisha Tadimalla \n", - "41 Lucy Kershaw \n", - "42 Sirisha Tadimalla \n", - "43 Michael Thrippleton \n", - "44 Michael Thrippleton \n", - "45 Lucy Kershaw \n", - "46 Ole Gunnar Johansen \n", - "47 Michael Thrippleton \n", - "48 Laura Bell \n", - "49 Oliver Gurney-Champion, Matthew Orton \n", - "50 Oliver Gurney-Champion, Matthew Orton \n", - "51 Sirisha Tadimalla \n", - "52 Oliver Gurney-Champion, Matthew Orton \n", - "53 Lucy Kershaw \n", - "54 Sirisha Tadimalla \n", - "55 Michael Thrippleton \n", - "56 Michael Berks \n", - "57 Laura Bell \n", - "58 Michael Thrippleton \n", - "59 Sirisha Tadimalla \n", - "60 Oliver Gurney-Champion, Matthew Orton \n", - "61 Laura Bell \n", - "62 Michael Thrippleton \n", - "63 Sirisha Tadimalla \n", - "64 Michael Thrippleton \n", - "65 Oliver Gurney-Champion, Matthew Orton \n", - "66 Zaki Ahmed \n", - "67 Sudarshan Ragunathan \n", - "68 Jesper Browall, Jonathan Arvidsson \n", - "69 Sudarshan Ragunathan \n", - "70 Laura Bell \n", - "71 Laura Bell \n", - "72 Sudarshan Ragunathan \n", - "73 Laura Bell \n", - "74 Laura Bell \n", - "\n", - " Institution Tester \\\n", - "0 University of Edinburgh, UK tbd \n", - "1 University of Edinburgh, UK tbd \n", - "2 University of Edinburgh, UK tbd \n", - "3 Amsterdam University Medical Center, the Nethe... tbd \n", - "4 University of Edinburgh, UK tbd \n", - "5 University of Manchester, UK tbd \n", - "6 Amsterdam University Medical Center, the Nethe... tbd \n", - "7 Amsterdam University Medical Center, the Nethe... tbd \n", - "8 the Netherlands Cancer Institute, the Netherlands JK/PvH \n", - "9 Amsterdam University Medical Center, the Nethe... JK/PvH \n", - "10 University of Manchester, UK tbd \n", - "11 University of Oslo, Norway tbd \n", - "12 University of Sydney, Australia JK/PvH \n", - "13 Amsterdam University Medical Center, the Nethe... JK/PvH \n", - "14 the Netherlands Cancer Institute, the Netherlands JK/PvH \n", - "15 University of Edinburgh, UK JK/PvH \n", - "16 University of Manchester, UK JK/PvH \n", - "17 University of Edinburgh, UK tbd \n", - "18 University of Sydney, Australia JK/PvH \n", - "19 University of Manchester, UK tbd \n", - "20 University of Sydney, Australia tbd \n", - "21 University of Edinburgh, UK tbd \n", - "22 University of Oslo, Norway tbd \n", - "23 University of Edinburgh, UK tbd \n", - "24 University of Manchester, UK ST/OGC \n", - "25 University of Manchester, UK ST/OGC \n", - "26 University of Edinburgh, UK tbd \n", - "27 University of Edinburgh, UK tbd \n", - "28 University of Edinburgh, UK tbd \n", - "29 University of Manchester, UK ST/OGC \n", - "30 University of Sydney, Australia tbd \n", - "31 University of Sydney, Australia tbd \n", - "32 University of Manchester, UK ST/OGC \n", - "33 University of Sydney, Australia tbd \n", - "34 University of Edinburgh, UK ST/OGC \n", - "35 University of Sydney, Australia ST/OGC \n", - "36 Amsterdam University Medical Center, the Nethe... ST/OGC \n", - "37 University of Oslo, Norway ST/OGC \n", - "38 University of Edinburgh, UK ST/OGC \n", - "39 University of Manchester, UK ST/OGC \n", - "40 University of Sydney, Australia tbd \n", - "41 University of Edinburgh, UK tbd \n", - "42 University of Sydney, Australia tbd \n", - "43 University of Edinburgh, UK tbd \n", - "44 University of Edinburgh, UK tbd \n", - "45 University of Edinburgh, UK ST/OGC \n", - "46 University of Oslo, Norway ST/OGC \n", - "47 University of Edinburgh, UK ST/OGC \n", - "48 Barrow Neurological Institute, USA ST/OGC \n", - "49 Amsterdam University Medical Center, the Nethe... tbd \n", - "50 Amsterdam University Medical Center, the Nethe... tbd \n", - "51 University of Sydney, Australia tbd \n", - "52 Amsterdam University Medical Center, the Nethe... tbd \n", - "53 University of Edinburgh, UK LK \n", - "54 University of Sydney, Australia LK \n", - "55 University of Edinburgh, UK LK \n", - "56 University of Manchester, UK LK \n", - "57 Barrow Neurological Institute, USA LK \n", - "58 University of Edinburgh, UK tbd \n", - "59 University of Sydney, Australia tbd \n", - "60 Amsterdam University Medical Center, the Nethe... tbd \n", - "61 Barrow Neurological Institute, USA tbd \n", - "62 University of Edinburgh, UK MJT \n", - "63 University of Sydney, Australia MJT \n", - "64 University of Edinburgh, UK MJT \n", - "65 Amsterdam University Medical Center, the Nethe... MJT \n", - "66 McGill University, Canada MJT \n", - "67 Barrow Neurological Institute, USA tbd \n", - "68 Sahlgrenska University Hospital and Gothenburg... tbd \n", - "69 Barrow Neurological Institute, USA tbd \n", - "70 Barrow Neurological Institute, USA tbd \n", - "71 Barrow Neurological Institute, USA tbd \n", - "72 Barrow Neurological Institute, USA tbd \n", - "73 Barrow Neurological Institute, USA tbd \n", - "74 Barrow Neurological Institute, USA tbd \n", - "\n", - " Test status (empty/in-progress/complete) Unnamed: 9 \n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 in-progress NaN \n", - "3 in-progress NaN \n", - "4 NaN NaN \n", - "5 NaN NaN \n", - "6 NaN NaN \n", - "7 NaN NaN \n", - "8 in-progress NaN \n", - "9 in-progress NaN \n", - "10 NaN NaN \n", - "11 NaN NaN \n", - "12 in-progress NaN \n", - "13 in-progress NaN \n", - "14 in-progress NaN \n", - "15 in-progress NaN \n", - "16 in-progress NaN \n", - "17 NaN NaN \n", - "18 in-progress NaN \n", - "19 NaN NaN \n", - "20 in-progress NaN \n", - "21 in-progress NaN \n", - "22 in-progress NaN \n", - "23 in-progress NaN \n", - "24 in-progress NaN \n", - "25 in-progress NaN \n", - "26 in-progress NaN \n", - "27 in-progress NaN \n", - "28 in-progress NaN \n", - "29 in-progress NaN \n", - "30 in-progress NaN \n", - "31 in-progress NaN \n", - "32 in-progress NaN \n", - "33 in-progress NaN \n", - "34 in-progress NaN \n", - "35 in-progress NaN \n", - "36 in-progress NaN \n", - "37 in-progress NaN \n", - "38 in-progress NaN \n", - "39 in-progress NaN \n", - "40 in-progress NaN \n", - "41 in-progress NaN \n", - "42 in-progress NaN \n", - "43 in-progress NaN \n", - "44 in-progress NaN \n", - "45 in-progress NaN \n", - "46 in-progress NaN \n", - "47 in-progress NaN \n", - "48 in-progress NaN \n", - "49 NaN NaN \n", - "50 in-progress NaN \n", - "51 NaN NaN \n", - "52 NaN NaN \n", - "53 completed NaN \n", - "54 completed NaN \n", - "55 completed NaN \n", - "56 completed NaN \n", - "57 completed NaN \n", - "58 NaN NaN \n", - "59 NaN NaN \n", - "60 NaN NaN \n", - "61 NaN NaN \n", - "62 in-progress NaN \n", - "63 complete NaN \n", - "64 complete NaN \n", - "65 in-progress NaN \n", - "66 complete NaN \n", - "67 NaN NaN \n", - "68 NaN NaN \n", - "69 NaN NaN \n", - "70 NaN NaN \n", - "71 NaN NaN \n", - "72 NaN NaN \n", - "73 NaN NaN \n", - "74 NaN NaN " - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df = pd.read_csv(\"../doc/code_contributions_record.csv\")\n", - "pd.set_option('display.max_rows', df.shape[0]+1)\n", - "df" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.0" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 87e2fb1d..6a203e32 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -7,5 +7,6 @@ mat73 scipy lmfit pandas +tabulate nilearn seaborn \ No newline at end of file