Merge pull request #18 from OSIPI/main

get brain_phantom branch up to date

Author: oscarjalnefjord

.github/workflows/unit_test.yml

@@ -33,4 +33,4 @@ jobs:
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
-          python -m pytest --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+          python -m pytest --doctest-modules --junitxml=junit/test-results.xml --cov=. --cov-report=xml --cov-report=html

.gitignore

@@ -1,2 +1,12 @@
 .idea*
-.github*
+.github*
+__pycache__/
+
+
+# Unit test / coverage reports
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+*.pyc

doc/code_contributions_record.csv

@@ -0,0 +1,18 @@
+Technique,Category,Subcategory,notes,subfolder,Link to source code,Authors,Institution,function/module,DOI,Tester,test status
+IVIM,Fitting,LSQ fitting,,OGC_AmsterdamUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/OGC_AmsterdamUMC/,Oliver Gurney-Champion,Amsterdam UMC,fit_least_squares/fit_least_squares_array,,tbd,
+IVIM,Fitting,segmented LSQ fitting,,OGC_AmsterdamUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/OGC_AmsterdamUMC/,Oliver Gurney-Champion,Amsterdam UMC,fit_segmented/fit_segmented_array,,tbd,
+Tri-exponential,Fitting,LSQ fitting,,OGC_AmsterdamUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/OGC_AmsterdamUMC/,Oliver Gurney-Champion,Amsterdam UMC,fit_least_squares_tri_exp/fit_least_squares_array_tri_exp,,tbd,
+Tri-exponential,Fitting,Segmented LSQ fitting,,OGC_AmsterdamUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/OGC_AmsterdamUMC/,Oliver Gurney-Champion,Amsterdam UMC,fit_segmented_tri_exp/fit_segmented_array_tri_exp,https://doi.org/10.3389/fphys.2022.942495,tbd,
+IVIM,Fitting,Bayesian,,OGC_AmsterdamUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/OGC_AmsterdamUMC/,Oliver Gurney-Champion/Sebastiano Barbieri,Amsterdam UMC,fit_bayesian_array,https://doi.org/10.1002/mrm.28852,tbd,
+IVIM,Fitting,two-step segmented fit approach,also includes ADC calculation as a separate function,PvH_KB_NKI,TF2.4_IVIM-MRI_CodeCollection/src/original/PvH_KB_NKI/,Petra van Houdt/Stefan Zijlema/Koen Baas,the Netherlands Cancer Institute,DWI_functions_standalone.py,https://doi.org/10.3389/fonc.2021.705964,tbd,
+IVIM,Fitting,two-step (segmented) LSQ fitting, cut-off chosen for brain data; option to fit IVIM with inversion recovery or without IR,PV_MUMC,TF2.4_IVIM-MRI_CodeCollection/src/original/PV_MUMC/,Paulien Voorter,Maastricht University Medical Center,two_step_IVIM_fit.py,,tbd,
+IVIM,Fitting,bi-exponential NLLS,Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_biexp.py,Ivan A. Rashid,Lund University,IvimModelBiexp,tba,tbd,
+IVIM,Fitting,2-step segmented NLLS,First estimates and fixes D before a bi-exponential NLLS fit. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_segmented_2step.py,Ivan A. Rashid,Lund University,IvimModelSegmented2Step,tba,tbd,
+IVIM,Fitting,3-step segmented NLLS,First estimates and fixes D followed by an estimate of D* followed by a bi-exponential NLLS fit. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_segmented_3step.py,Ivan A. Rashid,Lund University,IvimModelSegmented3Step,tba,tbd,
+IVIM,Fitting,2-step segmented NLLS,First estimates and fixes D. Subtracts the diffusion signal and estimated D*. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_subtracted.py,Ivan A. Rashid,Lund University,IvimModelSubtracted,tba,tbd,
+IVIM,Fitting,Variable projection,See referenced article. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_mix.py,Farooq et al. Modified by Ivan A. Rashid,Lund University,IvimModelVP,https://doi.org/10.1038/srep38927,tbd,
+IVIM,Fitting,Variable projection,See referenced article. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_topopro.py,Fadnavis et al. Modified by Ivan A. Rashid,Lund University,IvimModelTopoPro,https://doi.org/10.3389/fnins.2021.779025,tbd,
+IVIM,Fitting,Linear fit,Linear fit for D with extrapolation for f. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_linear.py,Modified by Ivan A. Rashid,Lund University,IvimModelLinear,tba,tbd,
+IVIM,Fitting,sIVIM fit,NLLS of the simplified IVIM model (sIVIM). Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_sivim.py,Modified by Ivan A. Rashid,Lund University,IvimModelsIVIM,tba,tbd,
+IVIM,Fitting,Segmented NLLS fitting,MATLAB code,OJ_GU,TF2.4_IVIM-MRI_CodeCollection/src/original/OJ_GU/,Oscar Jalnefjord,University of Gothenburg,IVIM_seg,https://doi.org/10.1007/s10334-018-0697-5,tbd,
+IVIM,Fitting,Bayesian,MATLAB code,OJ_GU,TF2.4_IVIM-MRI_CodeCollection/src/original/OJ_GU/,Oscar Jalnefjord,University of Gothenburg,IVIM_bayes,https://doi.org/10.1002/mrm.26783,tbd,

doc/guidelines_for_contributions.md

@@ -7,5 +7,5 @@ Follow the [general instructions for code constributions](create_local_copy_of_r
 For each contribution make sure to list the names and affiliations of all contributors of the particular code in the message of the pull request.
 
 ## Source code format
-Contributions of must be place in a folder named "Initials_Institution" under src/original, e.g. "src/original/OGC_AmsterdamUMC"
+Contributions must be place in a folder named "Initials_Institution" under src/original, e.g. "src/original/OGC_AmsterdamUMC"
 

phantoms/MR_XCAT_qMRI/README.md

@@ -0,0 +1 @@
+# MR_XCAT_qMRI