├── .gitattributes ├── LICENSE ├── README.md ├── README.org ├── code ├── 3rd │ ├── GetFullPath_20161216 │ │ ├── GetFullPath.c │ │ ├── GetFullPath.m │ │ ├── GetFullPath_ReadMe.txt │ │ ├── InstallMex.m │ │ ├── license.txt │ │ └── uTest_GetFullPath.m │ ├── MEDI_toolbox_20171107 │ │ ├── MEDI_GUI │ │ │ ├── GUIREADME.m │ │ │ └── MEDI_GUI.m │ │ ├── MEDI_set_path.m │ │ ├── README.m │ │ ├── UPDATES.m │ │ └── functions │ │ │ ├── Fit_ppm_complex.m │ │ │ ├── Fit_ppm_complex_TE.m │ │ │ ├── MEDI_L1.m │ │ │ ├── PDF.m │ │ │ ├── Read_Bruker_DICOM.m │ │ │ ├── Read_Bruker_DICOM_data.m │ │ │ ├── Read_Bruker_DICOM_real.m │ │ │ ├── Read_Bruker_raw.m │ │ │ ├── Read_DICOM.m │ │ │ ├── Read_GE_DICOM.m │ │ │ ├── Read_GE_DICOM_old.m │ │ │ ├── Read_Philips_DICOM.m │ │ │ ├── Read_Siemens_DICOM.m │ │ │ ├── Read_Siemens_DICOM_old.m │ │ │ ├── SMV.m │ │ │ ├── SMV_kernel.m │ │ │ ├── Visu3D.m │ │ │ ├── _LBV │ │ │ ├── LBV.m │ │ │ ├── mexMGv3.cpp │ │ │ ├── mexMGv3.mexw64 │ │ │ ├── mexMGv6.mexa64 │ │ │ ├── mexMGv6.mexmaci64 │ │ │ └── mexMGv6.mexw64 │ │ │ ├── _spurs_gc │ │ │ ├── README.txt │ │ │ ├── clique_energy_ho.m │ │ │ ├── energy_ho_3dW2.m │ │ │ ├── energy_ho_3dW2_pi.m │ │ │ ├── fit_IDEAL.m │ │ │ ├── fit_IDEAL_R2.m │ │ │ ├── heaviside.m │ │ │ ├── mf2.mexw64 │ │ │ ├── mincut.m │ │ │ ├── phase_unwrap_3d.m │ │ │ ├── runme_v2.m │ │ │ ├── spurs_gc.m │ │ │ ├── unwrap_unfat_3dN.m │ │ │ ├── unwrap_unfat_3dP.m │ │ │ └── unwrapping_gc.m │ │ │ ├── arlo.m │ │ │ ├── arlo_even.m │ │ │ ├── bdiv.m │ │ │ ├── bet2 │ │ │ ├── BET.m │ │ │ ├── arch.cpp │ │ │ ├── arch.h │ │ │ ├── bandmat.cpp │ │ │ ├── bet2.cpp │ │ │ ├── bet2.h │ │ │ ├── bet2.mexa64 │ │ │ ├── bet2.mexmaci64 │ │ │ ├── bet2.mexw64 │ │ │ ├── cluster.cpp │ │ │ ├── config.h │ │ │ ├── connectedcomp.cpp │ │ │ ├── controlw.h │ │ │ ├── cprob.h │ │ │ ├── dbh.h │ │ │ ├── evalue.cpp │ │ │ ├── fft.cpp │ │ │ ├── fsl │ │ │ │ ├── extras │ │ │ │ │ └── include │ │ │ │ │ │ └── newmat │ │ │ │ │ │ ├── boolean.h │ │ │ │ │ │ ├── include.h │ │ │ │ │ │ ├── myexcept.h │ │ │ │ │ │ ├── newmat.h │ │ │ │ │ │ ├── newmatap.h │ │ │ │ │ │ └── newmatio.h │ │ │ │ └── include │ │ │ │ │ ├── fslio │ │ │ │ │ ├── dbh.h │ │ │ │ │ └── fslio.h │ │ │ │ │ ├── meshclass │ │ │ │ │ ├── meshclass.h │ │ │ │ │ ├── point.h │ │ │ │ │ ├── profile.h │ │ │ │ │ └── pt_special.h │ │ │ │ │ ├── miscmaths │ │ │ │ │ ├── kernel.h │ │ │ │ │ ├── miscmaths.h │ │ │ │ │ └── splinterpolator.h │ │ │ │ │ ├── newimage │ │ │ │ │ ├── complexvolume.h │ │ │ │ │ ├── imfft.h │ │ │ │ │ ├── lazy.h │ │ │ │ │ ├── lazyiterators.h │ │ │ │ │ ├── newimage.h │ │ │ │ │ ├── newimageall.h │ │ │ │ │ ├── newimagefns.h │ │ │ │ │ ├── newimageio.h │ │ │ │ │ └── positerators.h │ │ │ │ │ ├── niftiio │ │ │ │ │ ├── nifti1.h │ │ │ │ │ └── nifti1_io.h │ │ │ │ │ ├── utils │ │ │ │ │ └── options.h │ │ │ │ │ └── znzlib │ │ │ │ │ ├── config.h │ │ │ │ │ └── znzlib.h │ │ │ ├── fslio.c │ │ │ ├── fslio.h │ │ │ ├── functions.cpp │ │ │ ├── jacobi.cpp │ │ │ ├── kernel.cpp │ │ │ ├── kernel.h │ │ │ ├── lazy.cpp │ │ │ ├── lazy.h │ │ │ ├── libprob.h │ │ │ ├── licence.html │ │ │ ├── matches.cpp │ │ │ ├── mesh.cpp │ │ │ ├── mesh.h │ │ │ ├── miscmaths.cpp │ │ │ ├── miscmaths.h │ │ │ ├── miscprob.h │ │ │ ├── mpoint.cpp │ │ │ ├── mpoint.h │ │ │ ├── myexcept.cpp │ │ │ ├── newfft.cpp │ │ │ ├── newimage.cpp │ │ │ ├── newimagefns.cpp │ │ │ ├── newmat1.cpp │ │ │ ├── newmat2.cpp │ │ │ ├── newmat3.cpp │ │ │ ├── newmat4.cpp │ │ │ ├── newmat5.cpp │ │ │ ├── newmat6.cpp │ │ │ ├── newmat7.cpp │ │ │ ├── newmat8.cpp │ │ │ ├── newmat9.cpp │ │ │ ├── newmatex.cpp │ │ │ ├── newmatrc.h │ │ │ ├── newmatrm.cpp │ │ │ ├── newmatrm.h │ │ │ ├── nifti1.h │ │ │ ├── nifti1_io.c │ │ │ ├── nifti1_io.h │ │ │ ├── parse.cpp │ │ │ ├── point.cpp │ │ │ ├── point.h │ │ │ ├── precisio.h │ │ │ ├── pt_special.cpp │ │ │ ├── pt_special.h │ │ │ ├── runmex.m │ │ │ ├── sort.cpp │ │ │ ├── submat.cpp │ │ │ ├── svd.cpp │ │ │ ├── triangle.cpp │ │ │ ├── triangle.h │ │ │ ├── znzlib.c │ │ │ └── znzlib.h │ │ │ ├── calfieldnoise.m │ │ │ ├── cdiv.m │ │ │ ├── cgrad.m │ │ │ ├── cgsolve.m │ │ │ ├── create_dicomattrs.m │ │ │ ├── dataterm_mask.m │ │ │ ├── dicom_findActualFilename.m │ │ │ ├── dicom_getFileDetails.m │ │ │ ├── dicomattrs.m │ │ │ ├── dipole_kernel.m │ │ │ ├── dipole_term.m │ │ │ ├── extract_CSF.m │ │ │ ├── fgrad.m │ │ │ ├── fitgrad.m │ │ │ ├── genMask.m │ │ │ ├── getnextfileno.m │ │ │ ├── gffun.m │ │ │ ├── gradient_mask.m │ │ │ ├── iField_correction.m │ │ │ ├── mexUnwrap.c │ │ │ ├── mexUnwrap.mexa64 │ │ │ ├── mexUnwrap.mexmaci64 │ │ │ ├── mexUnwrap.mexw64 │ │ │ ├── mexUnwrap1.c │ │ │ ├── mexUnwrap1.mexw64 │ │ │ ├── modifyMask.m │ │ │ ├── parse_QSM_input.m │ │ │ ├── phasorprep.m │ │ │ ├── sphere_kernel.m │ │ │ ├── store_QSM_results.m │ │ │ ├── unwrapLaplacian.m │ │ │ ├── unwrapPhase.m │ │ │ └── write_QSM_dir.m │ ├── NESTA_v1.1 │ │ ├── Analysis │ │ │ ├── PsiTransposeWFF.m │ │ │ ├── PsiWFF.m │ │ │ ├── analyze_tests.m │ │ │ ├── hadamard.c │ │ │ ├── hadamard.m │ │ │ ├── hadamard.map │ │ │ ├── hadamard.mexa64 │ │ │ ├── hadamard.mexglx │ │ │ ├── hadamard.mexmac │ │ │ ├── hadamard.mexmaci │ │ │ ├── hadamard.mexmaci64 │ │ │ ├── hadamard.mexw32 │ │ │ ├── makeSnr.m │ │ │ ├── make_window.m │ │ │ ├── pulseTrain.m │ │ │ ├── radar_signal.m │ │ │ ├── run_tests.m │ │ │ └── use_pulseTrain.m │ │ ├── Core_Nesterov.m │ │ ├── Core_Nesterov_UP.m │ │ ├── DemoAnalysis.m │ │ ├── DemoComplex.m │ │ ├── DemoContinuation.m │ │ ├── DemoContinuation.m~ │ │ ├── DemoNonProjector.m │ │ ├── DemoReweighting.m │ │ ├── DemoReweighting.m~ │ │ ├── DemoTV.m │ │ ├── DemoTV_UP.m │ │ ├── DemoUP.m │ │ ├── DemoUP.m~ │ │ ├── Misc │ │ │ ├── A_Subset.m │ │ │ ├── A_f.m │ │ │ ├── A_fhp.m │ │ │ ├── At_Subset.m │ │ │ ├── At_f.m │ │ │ ├── At_fhp.m │ │ │ ├── CGwrapper.m │ │ │ ├── LSQRwrapper.m │ │ │ ├── LineMask.m │ │ │ ├── MakeRDSquares.m │ │ │ ├── calctv.m │ │ │ ├── counter.m │ │ │ ├── msp_signal.m │ │ │ └── my_normest.m │ │ ├── NESTA.m │ │ ├── NESTA.m~ │ │ ├── NESTA_UP.m │ │ ├── RecPF_v1.1 │ │ │ ├── demo_RecPF.m │ │ │ ├── images │ │ │ │ ├── ortho1.jpg │ │ │ │ ├── ortho2.jpg │ │ │ │ ├── ortho3.jpg │ │ │ │ ├── ortho4.jpg │ │ │ │ ├── ortho5.jpg │ │ │ │ └── ortho6.jpg │ │ │ ├── readme.txt │ │ │ ├── solver │ │ │ │ ├── RecPF.asv │ │ │ │ ├── RecPF.m │ │ │ │ ├── RecPF_Modified.m │ │ │ │ └── RecPF_Modified.m~ │ │ │ └── utilities │ │ │ │ ├── MRImask.m │ │ │ │ ├── Wavedb1Phi.m │ │ │ │ ├── dctPhi.m │ │ │ │ ├── funcval.m │ │ │ │ ├── identityPhi.m │ │ │ │ ├── selectPF.m │ │ │ │ └── snr.m │ │ ├── Setup_Nesta.m │ │ ├── changeLog.txt │ │ └── fastProjection.m │ ├── NIfTI_20140122 │ │ ├── affine.m │ │ ├── bipolar.m │ │ ├── bresenham_line3d.m │ │ ├── clip_nii.m │ │ ├── collapse_nii_scan.m │ │ ├── examples.txt │ │ ├── expand_nii_scan.m │ │ ├── extra_nii_hdr.m │ │ ├── flip_lr.m │ │ ├── get_nii_frame.m │ │ ├── license.txt │ │ ├── load_nii.m │ │ ├── load_nii_ext.m │ │ ├── load_nii_hdr.m │ │ ├── load_nii_img.m │ │ ├── load_untouch0_nii_hdr.m │ │ ├── load_untouch_header_only.m │ │ ├── load_untouch_nii.m │ │ ├── load_untouch_nii_hdr.m │ │ ├── load_untouch_nii_img.m │ │ ├── make_ana.m │ │ ├── make_nii.m │ │ ├── mat_into_hdr.m │ │ ├── pad_nii.m │ │ ├── reslice_nii.m │ │ ├── rri_file_menu.m │ │ ├── rri_orient.m │ │ ├── rri_orient_ui.m │ │ ├── rri_select_file.m │ │ ├── rri_xhair.m │ │ ├── rri_zoom_menu.m │ │ ├── save_nii.m │ │ ├── save_nii_ext.m │ │ ├── save_nii_hdr.m │ │ ├── save_untouch0_nii_hdr.m │ │ ├── save_untouch_header_only.m │ │ ├── save_untouch_nii.m │ │ ├── save_untouch_nii_hdr.m │ │ ├── save_untouch_slice.m │ │ ├── test_niftiwriting.m │ │ ├── unxform_nii.m │ │ ├── verify_nii_ext.m │ │ ├── view_nii.m │ │ ├── view_nii_menu.m │ │ └── xform_nii.m │ ├── fwtoolbox_v1_code │ │ ├── README.txt │ │ ├── berglund │ │ │ ├── Common │ │ │ │ ├── dummyCoilCombine3D.m │ │ │ │ ├── trivialChoiceBetweenPhasorCandidates.m │ │ │ │ └── weightedSmoothing.m │ │ │ ├── FlexibleTwoPoint │ │ │ │ ├── README.txt │ │ │ │ ├── fw_i3cm0c_2flexiblepoint_berglund.m │ │ │ │ └── private │ │ │ │ │ ├── SolveLS_2point.m │ │ │ │ │ ├── checkParamsAndSetDefaults_FlexibleTwoPoint.m │ │ │ │ │ ├── getPhasorAtFirstEcho.m │ │ │ │ │ └── getPhasorCandidates.m │ │ │ ├── MultiSeedRegionGrowing │ │ │ │ ├── README.txt │ │ │ │ ├── RG.cpp │ │ │ │ ├── fw_i3cm0i_3point_berglund.m │ │ │ │ └── private │ │ │ │ │ ├── RG.mexa64 │ │ │ │ │ ├── RG.mexglx │ │ │ │ │ ├── RG.mexmaci64 │ │ │ │ │ ├── SolveLS.m │ │ │ │ │ ├── checkParamsAndSetDefaults_MultiSeedRegionGrowing.m │ │ │ │ │ ├── getMagnitudeWeight.m │ │ │ │ │ ├── getPhasorCandidates.m │ │ │ │ │ └── regionGrow.m │ │ │ ├── test_FlexibleTwoPoint.m │ │ │ └── test_MultiSeedRegionGrowing.m │ │ ├── bydder │ │ │ ├── cls4.m │ │ │ ├── decomposeGivenFieldMapAndDampings_commonPhase.m │ │ │ ├── fat_basis.m │ │ │ ├── getFatWaterSpectrum_massScale_fatByDoubleBonds.m │ │ │ └── test_bydder_111114.m │ │ ├── doneva │ │ │ ├── README_doneva.m │ │ │ ├── checkParamsAndSetDefaults_cswf.m │ │ │ ├── common │ │ │ │ ├── @DAMP │ │ │ │ │ ├── DA.asv │ │ │ │ │ ├── DAMP.m │ │ │ │ │ ├── ctranspose.m │ │ │ │ │ ├── mtimes.asv │ │ │ │ │ ├── mtimes.m │ │ │ │ │ └── private │ │ │ │ │ │ ├── conj_test.asv │ │ │ │ │ │ ├── conj_test.m │ │ │ │ │ │ ├── conjugation_test3.asv │ │ │ │ │ │ ├── dforward_op.asv │ │ │ │ │ │ ├── dforward_op.m │ │ │ │ │ │ ├── dforward_opH.asv │ │ │ │ │ │ ├── dforward_opH.m │ │ │ │ │ │ ├── forward1.asv │ │ │ │ │ │ ├── forward1_d.asv │ │ │ │ │ │ └── forward1_t.asv │ │ │ │ ├── @FD1OP │ │ │ │ │ ├── FD1OP.m │ │ │ │ │ ├── ctranspose.m │ │ │ │ │ ├── mtimes.m │ │ │ │ │ └── private │ │ │ │ │ │ ├── D.asv │ │ │ │ │ │ ├── D.m │ │ │ │ │ │ └── D_t.m │ │ │ │ ├── @FD2OP │ │ │ │ │ ├── FD2OP.m │ │ │ │ │ ├── ctranspose.m │ │ │ │ │ ├── mtimes.m │ │ │ │ │ └── private │ │ │ │ │ │ ├── D2.m │ │ │ │ │ │ └── D2_t.m │ │ │ │ ├── @Wavelet_TT │ │ │ │ │ ├── Wavelet_TT.m │ │ │ │ │ ├── ctranspose.m │ │ │ │ │ └── mtimes.m │ │ │ │ ├── @p2DFT │ │ │ │ │ ├── ctranspose.m │ │ │ │ │ ├── mtimes.m │ │ │ │ │ ├── p2DFT.m │ │ │ │ │ └── size.m │ │ │ │ ├── crop.m │ │ │ │ ├── fft2c.m │ │ │ │ ├── ifft2c.m │ │ │ │ └── zpad.m │ │ │ ├── create_synthetic │ │ │ │ └── createSynthetic_kSpace.m │ │ │ ├── fw_k2cs0i_3point_doneva_cswf.m │ │ │ ├── methods │ │ │ │ ├── forward_op_mp1.m │ │ │ │ ├── forward_op_mp1_H.m │ │ │ │ ├── locatemins_outer1.asv │ │ │ │ ├── locatemins_outer1.m │ │ │ │ ├── nonlin_cg.m │ │ │ │ ├── nonlin_cg_gn.m │ │ │ │ ├── objective_gn1.m │ │ │ │ ├── preobjective_gn.m │ │ │ │ ├── rm2d2.asv │ │ │ │ ├── rm2d2.m │ │ │ │ ├── wfcs.asv │ │ │ │ └── wfcs.m │ │ │ ├── parameter_initialization │ │ │ │ ├── initializecg_cs.m │ │ │ │ └── initializecg_wf.m │ │ │ ├── testSynthetic_doneva.m │ │ │ ├── test_doneva.m │ │ │ └── waveletMEX │ │ │ │ ├── FWT2_PO_TT2.c │ │ │ │ ├── FWT2_PO_TT2.mexa64 │ │ │ │ ├── FWT2_PO_TT2.mexglx │ │ │ │ ├── FWT2_PO_TT2.mexmaci64 │ │ │ │ ├── FWT2_PO_TT2.mexw32 │ │ │ │ ├── FWT2_PO_TT2.mexw64 │ │ │ │ ├── IWT2_PO_TT2.c │ │ │ │ ├── IWT2_PO_TT2.mexa64 │ │ │ │ ├── IWT2_PO_TT2.mexglx │ │ │ │ ├── IWT2_PO_TT2.mexmaci64 │ │ │ │ ├── IWT2_PO_TT2.mexw32 │ │ │ │ ├── IWT2_PO_TT2.mexw64 │ │ │ │ ├── MakeONFilter.m │ │ │ │ ├── downhi.c │ │ │ │ ├── downlo.c │ │ │ │ ├── mirrorfilt.c │ │ │ │ ├── uphi.c │ │ │ │ ├── uplo.c │ │ │ │ └── wavelab.h │ │ ├── eggers │ │ │ ├── README_120116.txt │ │ │ ├── checkParamsAndSetDefaults_cpr.asv │ │ │ ├── checkParamsAndSetDefaults_cpr.m │ │ │ ├── compute_constant_density_spiral_density.m │ │ │ ├── compute_constant_density_spiral_trajectory.m │ │ │ ├── cpr.asv │ │ │ ├── cpr.m │ │ │ ├── eggers_data │ │ │ │ └── README_eggers_data.txt │ │ │ ├── test_eggers_cpr.asv │ │ │ └── test_eggers_cpr.m │ │ ├── fwtoolboxTest.m │ │ ├── gui │ │ │ ├── freezeColors │ │ │ │ ├── Contents.m │ │ │ │ ├── demo │ │ │ │ │ └── html │ │ │ │ │ │ └── freezeColors_pub.html │ │ │ │ ├── freezeColors.m │ │ │ │ ├── license.txt │ │ │ │ ├── test │ │ │ │ │ └── test_main.m │ │ │ │ └── unfreezeColors.m │ │ │ └── fw_gui.m │ │ ├── hernando │ │ │ ├── #test_hernando_111110.m# │ │ │ ├── README_hernando.txt │ │ │ ├── common │ │ │ │ ├── #decomposeGivenFieldMapAndDampings.m# │ │ │ │ ├── coilCombine.m │ │ │ │ ├── coilCombine3D.m │ │ │ │ ├── computeFF.m │ │ │ │ ├── computeResidual.m │ │ │ │ ├── decomposeGivenFieldMapAndDampings.m │ │ │ │ ├── estimateR2starGivenFieldmap.m │ │ │ │ ├── findLocalMinima.m │ │ │ │ ├── getPhiMatrixMultipeak.m │ │ │ │ └── getQuadraticApprox.m │ │ │ ├── create_synthetic │ │ │ │ └── createSynthetic_imageSpace.m │ │ │ ├── descent │ │ │ │ ├── checkParamsAndSetDefaults_optimtransfer.m │ │ │ │ └── fw_i2cm0i_3plusploint_hernando_optimtransfer.m │ │ │ ├── graphcut │ │ │ │ ├── #fw_i2cm1i_3pluspoint_hernando_graphcut.m# │ │ │ │ ├── checkParamsAndSetDefaults_graphcut.m │ │ │ │ ├── createExpansionGraphVARPRO_fast.m │ │ │ │ ├── fw_i2cm1i_3pluspoint_hernando_graphcut.m │ │ │ │ └── graphCutIterations.m │ │ │ ├── matlab_bgl │ │ │ │ ├── .project │ │ │ │ ├── @inplace │ │ │ │ │ ├── assign.m │ │ │ │ │ ├── display.m │ │ │ │ │ ├── double.m │ │ │ │ │ ├── end.m │ │ │ │ │ ├── inplace.m │ │ │ │ │ ├── size.m │ │ │ │ │ ├── subsasgn.m │ │ │ │ │ └── subsref.m │ │ │ │ ├── @ipdouble │ │ │ │ │ └── ipdouble.m │ │ │ │ ├── @ipint32 │ │ │ │ │ └── ipint32.m │ │ │ │ ├── Contents.m │ │ │ │ ├── all_shortest_paths.m │ │ │ │ ├── astar_search.m │ │ │ │ ├── bellman_ford_sp.m │ │ │ │ ├── betweenness_centrality.m │ │ │ │ ├── bfs.m │ │ │ │ ├── biconnected_components.m │ │ │ │ ├── boyer_myrvold_planarity_test.m │ │ │ │ ├── breadth_first_search.m │ │ │ │ ├── chrobak_payne_straight_line_drawing.m │ │ │ │ ├── circle_graph_layout.m │ │ │ │ ├── clique_graph.m │ │ │ │ ├── clustering_coefficients.m │ │ │ │ ├── combine_visitors.m │ │ │ │ ├── components.m │ │ │ │ ├── core_numbers.m │ │ │ │ ├── custom │ │ │ │ │ ├── dijkstra_all_sp.m │ │ │ │ │ └── path_histogram.m │ │ │ │ ├── cycle_graph.m │ │ │ │ ├── dag_sp.m │ │ │ │ ├── depth_first_search.m │ │ │ │ ├── dfs.m │ │ │ │ ├── dijkstra_sp.m │ │ │ │ ├── doc │ │ │ │ │ ├── changed.txt │ │ │ │ │ ├── html │ │ │ │ │ │ ├── changes.html │ │ │ │ │ │ ├── core_numbers_example │ │ │ │ │ │ │ └── core_numbers_example.html │ │ │ │ │ │ ├── faq.html │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ ├── new_in_3 │ │ │ │ │ │ │ └── new_in_3_0.html │ │ │ │ │ │ ├── new_in_4 │ │ │ │ │ │ │ └── new_in_4_0.html │ │ │ │ │ │ ├── old.html │ │ │ │ │ │ ├── planar_graphs │ │ │ │ │ │ │ └── planar_graphs.html │ │ │ │ │ │ ├── record_alg │ │ │ │ │ │ │ └── record_alg.html │ │ │ │ │ │ ├── red_black │ │ │ │ │ │ │ └── red_black.html │ │ │ │ │ │ ├── reweighted_graphs │ │ │ │ │ │ │ └── reweighted_graphs.html │ │ │ │ │ │ ├── site.css │ │ │ │ │ │ └── style.css │ │ │ │ │ ├── mxdom2mbgl-html.xsl │ │ │ │ │ └── write_examples_html.m │ │ │ │ ├── edge_weight_index.m │ │ │ │ ├── edge_weight_vector.m │ │ │ │ ├── edmonds_maximum_cardinality_matching.m │ │ │ │ ├── edmunds_karp_max_flow.m │ │ │ │ ├── erdos_reyni.m │ │ │ │ ├── examples │ │ │ │ │ ├── approx_multiway_cut.m │ │ │ │ │ ├── bacon_numbers.m │ │ │ │ │ ├── bfs_example.m │ │ │ │ │ ├── bfs_in_mbgl.m │ │ │ │ │ ├── bfs_in_mbgl_efficient.m │ │ │ │ │ ├── core_numbers_example.m │ │ │ │ │ ├── dfs_example.m │ │ │ │ │ ├── edge_index_example.m │ │ │ │ │ ├── max_flow_example.m │ │ │ │ │ ├── multiway_example.m │ │ │ │ │ ├── new_in_3_0.m │ │ │ │ │ ├── new_in_4_0.m │ │ │ │ │ ├── planar_graphs.m │ │ │ │ │ ├── record_alg.m │ │ │ │ │ ├── red_black.m │ │ │ │ │ └── reweighted_graphs.m │ │ │ │ ├── floyd_warshall_all_sp.m │ │ │ │ ├── fruchterman_reingold_force_directed_layout.m │ │ │ │ ├── grid_graph.m │ │ │ │ ├── gursoy_atun_layout.m │ │ │ │ ├── indexed_sparse.m │ │ │ │ ├── is_kuratowski_graph.m │ │ │ │ ├── is_straight_line_drawing.m │ │ │ │ ├── johnson_all_sp.m │ │ │ │ ├── kamada_kawai_spring_layout.m │ │ │ │ ├── kolmogorov_max_flow.m │ │ │ │ ├── kruskal_mst.m │ │ │ │ ├── kuratowski_subgraph.m │ │ │ │ ├── lengauer_tarjan_dominator_tree.m │ │ │ │ ├── libmbgl │ │ │ │ │ ├── ccfiles.sh │ │ │ │ │ ├── compile-linux-32.sh │ │ │ │ │ ├── compile-linux-64-large.sh │ │ │ │ │ ├── compile-linux-64.sh │ │ │ │ │ ├── compile-macosx-intel-32.sh │ │ │ │ │ ├── compile-macosx-ppc-32.sh │ │ │ │ │ ├── compile-win32.bat │ │ │ │ │ ├── compile-win64.bat │ │ │ │ │ ├── components.cc │ │ │ │ │ ├── crm_graph.hpp │ │ │ │ │ ├── include │ │ │ │ │ │ ├── matlab_bgl.h │ │ │ │ │ │ └── matlab_bgl_types.h │ │ │ │ │ ├── layouts.cc │ │ │ │ │ ├── libmbgl-macosx-intel-64-large.a │ │ │ │ │ ├── libmbgl.sln │ │ │ │ │ ├── libmbgl.vcproj │ │ │ │ │ ├── libmbgl_test │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── fr_layout_test.cc │ │ │ │ │ │ ├── layout_funcs_test.cc │ │ │ │ │ │ ├── libmbgl_funcs_test.cc │ │ │ │ │ │ ├── libmbgl_funcs_test.h │ │ │ │ │ │ ├── libmbgl_test.cc │ │ │ │ │ │ ├── libmbgl_test.vcproj │ │ │ │ │ │ ├── planar_funcs_test.cc │ │ │ │ │ │ ├── planar_is_straight_line_test.cc │ │ │ │ │ │ ├── planar_ksubgraph_test.cc │ │ │ │ │ │ ├── property_map_test.cc │ │ │ │ │ │ ├── simple_prop_map_test.cc │ │ │ │ │ │ ├── simple_prop_map_test_2.cc │ │ │ │ │ │ ├── simple_prop_map_test_3.cc │ │ │ │ │ │ └── simple_prop_map_test_4.cc │ │ │ │ │ ├── libmbgl_util.hpp │ │ │ │ │ ├── max_flow.cc │ │ │ │ │ ├── orderings.cc │ │ │ │ │ ├── planar.cc │ │ │ │ │ ├── searches.cc │ │ │ │ │ ├── shortest_path.cc │ │ │ │ │ ├── spanning_trees.cc │ │ │ │ │ ├── statistics.cc │ │ │ │ │ ├── stop_visitors.hpp │ │ │ │ │ ├── visitor_macros.hpp │ │ │ │ │ └── yasmic │ │ │ │ │ │ ├── .sconsign │ │ │ │ │ │ ├── bgl_kcore.hpp │ │ │ │ │ │ ├── binary_ifstream_graph.hpp │ │ │ │ │ │ ├── binary_ifstream_matrix.hpp │ │ │ │ │ │ ├── bind_utility.hpp │ │ │ │ │ │ ├── boost_mod │ │ │ │ │ │ ├── .sconsign │ │ │ │ │ │ ├── bellman_ford_shortest_paths.hpp │ │ │ │ │ │ ├── betweenness_centrality.hpp │ │ │ │ │ │ ├── chrobak_payne_drawing.hpp │ │ │ │ │ │ ├── core_numbers.hpp │ │ │ │ │ │ ├── floyd_warshall_shortest.hpp │ │ │ │ │ │ ├── fruchterman_reingold.hpp │ │ │ │ │ │ ├── gzip.hpp │ │ │ │ │ │ ├── integer_extra.hpp │ │ │ │ │ │ ├── is_straight_line_drawing.hpp │ │ │ │ │ │ ├── johnson_all_pairs_shortest.hpp │ │ │ │ │ │ ├── kolmogorov_max_flow.hpp │ │ │ │ │ │ ├── kruskal_min_spanning_tree.hpp │ │ │ │ │ │ └── zlib.cpp │ │ │ │ │ │ ├── bvgraph_matrix.hpp │ │ │ │ │ │ ├── cluto_ifstream_matrix.hpp │ │ │ │ │ │ ├── compressed_row_matrix.hpp │ │ │ │ │ │ ├── compressed_row_matrix_graph.hpp │ │ │ │ │ │ ├── generic_matrix_operations.hpp │ │ │ │ │ │ ├── graph_ifstream_matrix.hpp │ │ │ │ │ │ ├── ifstream_as_matrix.hpp │ │ │ │ │ │ ├── ifstream_matrix.hpp │ │ │ │ │ │ ├── indexed_list.hpp │ │ │ │ │ │ ├── indexed_list.old.hpp │ │ │ │ │ │ ├── indexed_list_as_graph.hpp │ │ │ │ │ │ ├── istream_as_matrix.hpp │ │ │ │ │ │ ├── iterator_utility.hpp │ │ │ │ │ │ ├── matrix_row_col_graph.hpp │ │ │ │ │ │ ├── nonzero_union.hpp │ │ │ │ │ │ ├── simple_csr_matrix.hpp │ │ │ │ │ │ ├── simple_csr_matrix_as_graph.hpp │ │ │ │ │ │ ├── simple_row_and_column_matrix.hpp │ │ │ │ │ │ ├── simple_row_and_column_matrix_as_graph.hpp │ │ │ │ │ │ ├── smatrix_traits.hpp │ │ │ │ │ │ ├── transpose_matrix.hpp │ │ │ │ │ │ ├── tuple_utility.hpp │ │ │ │ │ │ ├── undir_simple_csr_matrix.hpp │ │ │ │ │ │ ├── undir_simple_csr_matrix_as_graph.hpp │ │ │ │ │ │ ├── util │ │ │ │ │ │ ├── .sconsign │ │ │ │ │ │ ├── crm_matrix.hpp │ │ │ │ │ │ ├── filtered_matrix.hpp │ │ │ │ │ │ ├── load_crm_graph.hpp │ │ │ │ │ │ ├── load_crm_matrix.hpp │ │ │ │ │ │ ├── write_matrix.hpp │ │ │ │ │ │ └── write_petsc_matrix.hpp │ │ │ │ │ │ ├── verbose_util.hpp │ │ │ │ │ │ ├── yasmic.cbp │ │ │ │ │ │ ├── yasmic.layout │ │ │ │ │ │ ├── yasmic.vcproj │ │ │ │ │ │ ├── yasmic.vcproj.DUALCORE.mithandor.user │ │ │ │ │ │ └── yasmic.vcproj.MITHANDOR.mithandor.user │ │ │ │ ├── make_biconnected_planar.m │ │ │ │ ├── make_connected.m │ │ │ │ ├── make_maximal_planar.m │ │ │ │ ├── matching.m │ │ │ │ ├── max_flow.m │ │ │ │ ├── maximal_matching.m │ │ │ │ ├── mst.m │ │ │ │ ├── num_edges.m │ │ │ │ ├── num_vertices.m │ │ │ │ ├── path_from_pred.m │ │ │ │ ├── planar_canonical_ordering.m │ │ │ │ ├── prim_mst.m │ │ │ │ ├── private │ │ │ │ │ ├── astar_search_mex.c │ │ │ │ │ ├── astar_search_mex.mexa64 │ │ │ │ │ ├── astar_search_mex.mexglx │ │ │ │ │ ├── astar_search_mex.mexmac │ │ │ │ │ ├── astar_search_mex.mexmaci │ │ │ │ │ ├── astar_search_mex.mexmaci64 │ │ │ │ │ ├── astar_search_mex.mexw32 │ │ │ │ │ ├── astar_search_mex.mexw64 │ │ │ │ │ ├── betweenness_centrality_mex.c │ │ │ │ │ ├── betweenness_centrality_mex.mexa64 │ │ │ │ │ ├── betweenness_centrality_mex.mexglx │ │ │ │ │ ├── betweenness_centrality_mex.mexmac │ │ │ │ │ ├── betweenness_centrality_mex.mexmaci │ │ │ │ │ ├── betweenness_centrality_mex.mexmaci64 │ │ │ │ │ ├── betweenness_centrality_mex.mexw32 │ │ │ │ │ ├── betweenness_centrality_mex.mexw64 │ │ │ │ │ ├── bfs_dfs_vis_mex.c │ │ │ │ │ ├── bfs_dfs_vis_mex.mexa64 │ │ │ │ │ ├── bfs_dfs_vis_mex.mexglx │ │ │ │ │ ├── bfs_dfs_vis_mex.mexmac │ │ │ │ │ ├── bfs_dfs_vis_mex.mexmaci │ │ │ │ │ ├── bfs_dfs_vis_mex.mexmaci64 │ │ │ │ │ ├── bfs_dfs_vis_mex.mexw32 │ │ │ │ │ ├── bfs_dfs_vis_mex.mexw64 │ │ │ │ │ ├── bfs_mex.c │ │ │ │ │ ├── bfs_mex.mexa64 │ │ │ │ │ ├── bfs_mex.mexglx │ │ │ │ │ ├── bfs_mex.mexmac │ │ │ │ │ ├── bfs_mex.mexmaci │ │ │ │ │ ├── bfs_mex.mexmaci64 │ │ │ │ │ ├── bfs_mex.mexw32 │ │ │ │ │ ├── bfs_mex.mexw64 │ │ │ │ │ ├── biconnected_components_mex.c │ │ │ │ │ ├── biconnected_components_mex.mexa64 │ │ │ │ │ ├── biconnected_components_mex.mexglx │ │ │ │ │ ├── biconnected_components_mex.mexmac │ │ │ │ │ ├── biconnected_components_mex.mexmaci │ │ │ │ │ ├── biconnected_components_mex.mexmaci64 │ │ │ │ │ ├── biconnected_components_mex.mexw32 │ │ │ │ │ ├── biconnected_components_mex.mexw64 │ │ │ │ │ ├── check_matlab_bgl.m │ │ │ │ │ ├── clustering_coefficients_mex.c │ │ │ │ │ ├── clustering_coefficients_mex.mexa64 │ │ │ │ │ ├── clustering_coefficients_mex.mexglx │ │ │ │ │ ├── clustering_coefficients_mex.mexmac │ │ │ │ │ ├── clustering_coefficients_mex.mexmaci │ │ │ │ │ ├── clustering_coefficients_mex.mexmaci64 │ │ │ │ │ ├── clustering_coefficients_mex.mexw32 │ │ │ │ │ ├── clustering_coefficients_mex.mexw64 │ │ │ │ │ ├── common_functions.h │ │ │ │ │ ├── common_macros.h │ │ │ │ │ ├── compile.m │ │ │ │ │ ├── components_mex.c │ │ │ │ │ ├── components_mex.mexa64 │ │ │ │ │ ├── components_mex.mexglx │ │ │ │ │ ├── components_mex.mexmac │ │ │ │ │ ├── components_mex.mexmaci │ │ │ │ │ ├── components_mex.mexmaci64 │ │ │ │ │ ├── components_mex.mexw32 │ │ │ │ │ ├── components_mex.mexw64 │ │ │ │ │ ├── core_numbers_mex.c │ │ │ │ │ ├── core_numbers_mex.mexa64 │ │ │ │ │ ├── core_numbers_mex.mexglx │ │ │ │ │ ├── core_numbers_mex.mexmac │ │ │ │ │ ├── core_numbers_mex.mexmaci │ │ │ │ │ ├── core_numbers_mex.mexmaci64 │ │ │ │ │ ├── core_numbers_mex.mexw32 │ │ │ │ │ ├── core_numbers_mex.mexw64 │ │ │ │ │ ├── dfs_mex.c │ │ │ │ │ ├── dfs_mex.mexa64 │ │ │ │ │ ├── dfs_mex.mexglx │ │ │ │ │ ├── dfs_mex.mexmac │ │ │ │ │ ├── dfs_mex.mexmaci │ │ │ │ │ ├── dfs_mex.mexmaci64 │ │ │ │ │ ├── dfs_mex.mexw32 │ │ │ │ │ ├── dfs_mex.mexw64 │ │ │ │ │ ├── dominator_tree_mex.c │ │ │ │ │ ├── dominator_tree_mex.mexa64 │ │ │ │ │ ├── dominator_tree_mex.mexglx │ │ │ │ │ ├── dominator_tree_mex.mexmac │ │ │ │ │ ├── dominator_tree_mex.mexmaci │ │ │ │ │ ├── dominator_tree_mex.mexmaci64 │ │ │ │ │ ├── dominator_tree_mex.mexw32 │ │ │ │ │ ├── dominator_tree_mex.mexw64 │ │ │ │ │ ├── expand_macros.h │ │ │ │ │ ├── fruchterman_reingold_mex.c │ │ │ │ │ ├── fruchterman_reingold_mex.mexa64 │ │ │ │ │ ├── fruchterman_reingold_mex.mexglx │ │ │ │ │ ├── fruchterman_reingold_mex.mexmac │ │ │ │ │ ├── fruchterman_reingold_mex.mexmaci │ │ │ │ │ ├── fruchterman_reingold_mex.mexmaci64 │ │ │ │ │ ├── fruchterman_reingold_mex.mexw32 │ │ │ │ │ ├── fruchterman_reingold_mex.mexw64 │ │ │ │ │ ├── get_matlab_bgl_options.m │ │ │ │ │ ├── gursoy_atun_mex.c │ │ │ │ │ ├── gursoy_atun_mex.mexa64 │ │ │ │ │ ├── gursoy_atun_mex.mexglx │ │ │ │ │ ├── gursoy_atun_mex.mexmac │ │ │ │ │ ├── gursoy_atun_mex.mexmaci │ │ │ │ │ ├── gursoy_atun_mex.mexmaci64 │ │ │ │ │ ├── gursoy_atun_mex.mexw32 │ │ │ │ │ ├── gursoy_atun_mex.mexw64 │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.c │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexa64 │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexglx │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexmac │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexmaci │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexmaci64 │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexw32 │ │ │ │ │ ├── kamada_kawai_spring_layout_mex.mexw64 │ │ │ │ │ ├── matching_mex.c │ │ │ │ │ ├── matching_mex.mexa64 │ │ │ │ │ ├── matching_mex.mexglx │ │ │ │ │ ├── matching_mex.mexmac │ │ │ │ │ ├── matching_mex.mexmaci │ │ │ │ │ ├── matching_mex.mexmaci64 │ │ │ │ │ ├── matching_mex.mexw32 │ │ │ │ │ ├── matching_mex.mexw64 │ │ │ │ │ ├── matlab_bgl_all_sp_mex.c │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexa64 │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexglx │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexmac │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexmaci │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexmaci64 │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexw32 │ │ │ │ │ ├── matlab_bgl_all_sp_mex.mexw64 │ │ │ │ │ ├── matlab_bgl_sp_mex.c │ │ │ │ │ ├── matlab_bgl_sp_mex.mexa64 │ │ │ │ │ ├── matlab_bgl_sp_mex.mexglx │ │ │ │ │ ├── matlab_bgl_sp_mex.mexmac │ │ │ │ │ ├── matlab_bgl_sp_mex.mexmaci │ │ │ │ │ ├── matlab_bgl_sp_mex.mexmaci64 │ │ │ │ │ ├── matlab_bgl_sp_mex.mexw32 │ │ │ │ │ ├── matlab_bgl_sp_mex.mexw64 │ │ │ │ │ ├── max_flow_mex.c │ │ │ │ │ ├── max_flow_mex.mexa64 │ │ │ │ │ ├── max_flow_mex.mexglx │ │ │ │ │ ├── max_flow_mex.mexmac │ │ │ │ │ ├── max_flow_mex.mexmaci │ │ │ │ │ ├── max_flow_mex.mexmaci64 │ │ │ │ │ ├── max_flow_mex.mexw32 │ │ │ │ │ ├── max_flow_mex.mexw64 │ │ │ │ │ ├── merge_options.m │ │ │ │ │ ├── merge_structs.m │ │ │ │ │ ├── mst_mex.c │ │ │ │ │ ├── mst_mex.mexa64 │ │ │ │ │ ├── mst_mex.mexglx │ │ │ │ │ ├── mst_mex.mexmac │ │ │ │ │ ├── mst_mex.mexmaci │ │ │ │ │ ├── mst_mex.mexmaci64 │ │ │ │ │ ├── mst_mex.mexw32 │ │ │ │ │ ├── mst_mex.mexw64 │ │ │ │ │ ├── path_from_pred_mex.c │ │ │ │ │ ├── path_from_pred_mex.mexa64 │ │ │ │ │ ├── path_from_pred_mex.mexglx │ │ │ │ │ ├── path_from_pred_mex.mexmac │ │ │ │ │ ├── path_from_pred_mex.mexmaci │ │ │ │ │ ├── path_from_pred_mex.mexmaci64 │ │ │ │ │ ├── path_from_pred_mex.mexw32 │ │ │ │ │ ├── path_from_pred_mex.mexw64 │ │ │ │ │ ├── planar_drawing_mex.c │ │ │ │ │ ├── planar_drawing_mex.mexa64 │ │ │ │ │ ├── planar_drawing_mex.mexglx │ │ │ │ │ ├── planar_drawing_mex.mexmac │ │ │ │ │ ├── planar_drawing_mex.mexmaci │ │ │ │ │ ├── planar_drawing_mex.mexmaci64 │ │ │ │ │ ├── planar_drawing_mex.mexw32 │ │ │ │ │ ├── planar_drawing_mex.mexw64 │ │ │ │ │ ├── planar_edges_mex.c │ │ │ │ │ ├── planar_edges_mex.mexa64 │ │ │ │ │ ├── planar_edges_mex.mexglx │ │ │ │ │ ├── planar_edges_mex.mexmac │ │ │ │ │ ├── planar_edges_mex.mexmaci │ │ │ │ │ ├── planar_edges_mex.mexmaci64 │ │ │ │ │ ├── planar_edges_mex.mexw32 │ │ │ │ │ ├── planar_edges_mex.mexw64 │ │ │ │ │ ├── planar_test_mex.c │ │ │ │ │ ├── planar_test_mex.mexa64 │ │ │ │ │ ├── planar_test_mex.mexglx │ │ │ │ │ ├── planar_test_mex.mexmac │ │ │ │ │ ├── planar_test_mex.mexmaci │ │ │ │ │ ├── planar_test_mex.mexmaci64 │ │ │ │ │ ├── planar_test_mex.mexw32 │ │ │ │ │ ├── planar_test_mex.mexw64 │ │ │ │ │ ├── test_matching_mex.c │ │ │ │ │ ├── test_matching_mex.mexa64 │ │ │ │ │ ├── test_matching_mex.mexglx │ │ │ │ │ ├── test_matching_mex.mexmac │ │ │ │ │ ├── test_matching_mex.mexmaci │ │ │ │ │ ├── test_matching_mex.mexmaci64 │ │ │ │ │ ├── test_matching_mex.mexw32 │ │ │ │ │ ├── test_matching_mex.mexw64 │ │ │ │ │ ├── todo.m │ │ │ │ │ ├── todo_3_0_release.m │ │ │ │ │ ├── topological_order_mex.c │ │ │ │ │ ├── topological_order_mex.mexa64 │ │ │ │ │ ├── topological_order_mex.mexglx │ │ │ │ │ ├── topological_order_mex.mexmac │ │ │ │ │ ├── topological_order_mex.mexmaci │ │ │ │ │ ├── topological_order_mex.mexmaci64 │ │ │ │ │ ├── topological_order_mex.mexw32 │ │ │ │ │ ├── topological_order_mex.mexw64 │ │ │ │ │ └── visitor_macros.h │ │ │ │ ├── push_relabel_max_flow.m │ │ │ │ ├── random_graph_layout.m │ │ │ │ ├── set_matlab_bgl_default.m │ │ │ │ ├── shortest_paths.m │ │ │ │ ├── star_graph.m │ │ │ │ ├── test │ │ │ │ │ ├── assert.m │ │ │ │ │ ├── rtest_1.m │ │ │ │ │ ├── rtest_2.m │ │ │ │ │ ├── rtest_3_cojocaru.m │ │ │ │ │ ├── rtest_5_henderson.m │ │ │ │ │ ├── rtest_6.m │ │ │ │ │ ├── rtest_7_karsi.m │ │ │ │ │ ├── rtest_all.m │ │ │ │ │ ├── test_all.m │ │ │ │ │ ├── test_benchmark.m │ │ │ │ │ ├── test_breadth_first_search.m │ │ │ │ │ ├── test_components.m │ │ │ │ │ ├── test_depth_first_search.m │ │ │ │ │ ├── test_examples.m │ │ │ │ │ ├── test_layouts.m │ │ │ │ │ ├── test_main.m │ │ │ │ │ ├── test_planar.m │ │ │ │ │ ├── test_searches.m │ │ │ │ │ ├── test_shortest_paths.m │ │ │ │ │ ├── test_spanning_trees.m │ │ │ │ │ ├── test_statistics.m │ │ │ │ │ └── test_trivial.m │ │ │ │ ├── test_dag.m │ │ │ │ ├── test_matching.m │ │ │ │ ├── test_planar_graph.m │ │ │ │ ├── topological_order.m │ │ │ │ ├── tree_from_pred.m │ │ │ │ └── wheel_graph.m │ │ │ ├── mixed_fitting │ │ │ │ ├── checkParamsAndSetDefaults_mixedfit.m │ │ │ │ └── fw_i2xm1c_3pluspoint_hernando_mixedfit.m │ │ │ ├── testSynthetic_hernando_111110.m │ │ │ └── test_hernando_111110.m │ │ ├── hu │ │ │ ├── README │ │ │ │ ├── README.m │ │ │ │ └── README.ppt │ │ │ ├── Support Functions │ │ │ │ ├── calcg.m │ │ │ │ ├── cofmass.m │ │ │ │ ├── coilCombine3D_back.m │ │ │ │ ├── coilCombine_back.m │ │ │ │ ├── euclidean.m │ │ │ │ ├── final_wf_decomp.m │ │ │ │ ├── getlowresdata.m │ │ │ │ ├── load_data.m │ │ │ │ ├── mip_hh.m │ │ │ │ ├── plot_fatpeaks.m │ │ │ │ ├── regiongrowloop.m │ │ │ │ ├── run_ideal.m │ │ │ │ ├── solveA.m │ │ │ │ ├── square_spiral.m │ │ │ │ ├── validity_checks.m │ │ │ │ └── validity_checks_multicoil.m │ │ │ ├── fw_i2cm0c_3pluspoint_RGsinglecoil_hu.m │ │ │ ├── plottrajectory.m │ │ │ ├── test_fw_i2cm0c_3pluspoint_RGmulticoil.m │ │ │ └── test_fw_i2cm0c_3pluspoint_RGsinglecoil.m │ │ ├── lu │ │ │ ├── fw_3point_wm_goldSect.m │ │ │ ├── multiResSep │ │ │ │ ├── alphaFunc.m │ │ │ │ ├── batchSep.m │ │ │ │ ├── batchSepPfile.m │ │ │ │ ├── bestInitMap.m │ │ │ │ ├── calc_deltaTE.m │ │ │ │ ├── calc_mixMat.m │ │ │ │ ├── check_propgPsi.m │ │ │ │ ├── combMedianPsi.m │ │ │ │ ├── combMultiCoil.m │ │ │ │ ├── est_fieldMap.m │ │ │ │ ├── example.m │ │ │ │ ├── findFieldMap.m │ │ │ │ ├── getAlpha.m │ │ │ │ ├── getSepResult.m │ │ │ │ ├── get_contourInd.m │ │ │ │ ├── get_linPhaseMat.m │ │ │ │ ├── get_startCentroidXY.m │ │ │ │ ├── get_startPixInd.m │ │ │ │ ├── golden.m │ │ │ │ ├── goldenAlpha.m │ │ │ │ ├── imMagMask.m │ │ │ │ ├── init_pyramid.m │ │ │ │ ├── kspaceCorr.m │ │ │ │ ├── lsSep_wf.m │ │ │ │ ├── multiGolden.m │ │ │ │ ├── multiResSep.m │ │ │ │ ├── propg_psi.m │ │ │ │ ├── rfunc.m │ │ │ │ ├── smooth_fmap.m │ │ │ │ ├── srcCoilCombineGEMR1.m │ │ │ │ └── wlsFit.m │ │ │ └── testSynthetic_wenmiao_111219.m │ │ ├── pineda_bice │ │ │ ├── ReadAndRunMe.m │ │ │ ├── ReadAndRunMe_quick.m │ │ │ ├── buildSignals.m │ │ │ ├── fw_mcsim_2pluspoint.m │ │ │ ├── fw_nsa_2pluspoint.m │ │ │ ├── fw_nsa_map.m │ │ │ ├── getCRB.m │ │ │ ├── getCRBnorm.m │ │ │ └── test_2pi.m │ │ ├── runGUI.m │ │ ├── sharma │ │ │ ├── @B │ │ │ │ ├── B.asv │ │ │ │ ├── B.m │ │ │ │ ├── ctranspose.m │ │ │ │ ├── mtimes.asv │ │ │ │ └── mtimes.m │ │ │ ├── @Bspline │ │ │ │ ├── Bspline.m │ │ │ │ ├── Overlap_Wavelet.asv │ │ │ │ ├── ctranspose.m │ │ │ │ ├── mtimes.asv │ │ │ │ └── mtimes.m │ │ │ ├── README.txt │ │ │ ├── estimate_water_fat.m │ │ │ ├── fw_i2cm0i_3pluspoint_sharma.m │ │ │ ├── test_sharma_20111220.m │ │ │ ├── update_field_map.m │ │ │ └── utils │ │ │ │ ├── SDS_BSpline_Basis.m │ │ │ │ ├── SDS_Create_BSpline.asv │ │ │ │ ├── SDS_Create_BSpline.m │ │ │ │ ├── calculate_chemical_shift_encoding_matrix.m │ │ │ │ ├── coilCombine_old.m │ │ │ │ ├── error_check.m │ │ │ │ ├── fnlCg.asv │ │ │ │ ├── fnlCg.m │ │ │ │ └── init.m │ │ ├── tsao_jiang │ │ │ ├── ConvertSingleToMultipeakRecon.m │ │ │ ├── README.doc │ │ │ ├── fw_i2cm0c_3pluspoint_tsaojiang.m │ │ │ ├── fw_i2cs0c_3point_tsaojiang.m │ │ │ ├── fw_inputparams.m │ │ │ ├── fw_showresults.m │ │ │ ├── private │ │ │ │ ├── ChangeArraySize.m │ │ │ │ ├── CombineCoilImg.m │ │ │ │ ├── ComplexToRgb.m │ │ │ │ ├── ConvertSingleToMultipeakRecon.m │ │ │ │ ├── VerifyEchoTimes.m │ │ │ │ ├── dumpallvariables.m │ │ │ │ ├── fw_inputparams.txt │ │ │ │ ├── hierarchical_IDEAL_engine.c │ │ │ │ ├── hierarchical_IDEAL_engine.dll │ │ │ │ ├── hierarchical_IDEAL_engine.mexa64 │ │ │ │ ├── hierarchical_IDEAL_engine.mexglx │ │ │ │ ├── hierarchical_IDEAL_engine.mexmaci64 │ │ │ │ ├── hierarchical_IDEAL_engine.mexw32 │ │ │ │ ├── hierarchical_IDEAL_engine.mexw64 │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.c │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.dll │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.mexa64 │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.mexglx │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.mexmaci64 │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.mexw32 │ │ │ │ ├── hierarchical_IDEAL_engine_flexible.mexw64 │ │ │ │ ├── setthreshold.m │ │ │ │ ├── transformImageToKspace.m │ │ │ │ └── transformKspaceToImage.m │ │ │ ├── test │ │ │ │ ├── #testHierarchicalIDEALwithInvivo.m# │ │ │ │ ├── data │ │ │ │ │ └── WaterFatSilicon │ │ │ │ │ │ └── WaterFatSilicon.tif │ │ │ │ ├── private │ │ │ │ │ ├── createFatWaterPhantomData_tsaojiang.m │ │ │ │ │ ├── createSynthetic_imageSpace.m │ │ │ │ │ └── idealgradechotimes.m │ │ │ │ ├── testHierarchicalIDEALwithData.m │ │ │ │ ├── testHierarchicalIDEALwithInvivo.m │ │ │ │ └── testHierarchicalIDEALwithSynthetic.m │ │ │ └── testHierarchicalIDEAL.m │ │ ├── updates_log.txt │ │ └── wu │ │ │ ├── README.txt │ │ │ ├── ccrings_FW_fdLS.m │ │ │ ├── ccrings_FW_gcut.m │ │ │ ├── ccrings_FW_template.m │ │ │ ├── ccrlib │ │ │ ├── ccr_k2im.m │ │ │ ├── ccr_savecine.m │ │ │ ├── fdIDEAL.m │ │ │ ├── fw_k2cs0i_ccr_fdLS_wu.m │ │ │ ├── fw_k2cs1i_ccr_gcut_wu.m │ │ │ ├── fw_tttttt_ccr_imsp_wu.m │ │ │ └── getsubset.m │ │ │ └── grid2D │ │ │ ├── gr2dKB_mex.c │ │ │ ├── gr2dKB_mex.dll │ │ │ ├── gr2dKB_mex.mexa64 │ │ │ ├── gr2dKB_mex.mexglx │ │ │ ├── gr2dKB_mex.mexmaci │ │ │ ├── gr2dKB_mex.mexmaci64 │ │ │ ├── gr2dKB_mex.mexw64 │ │ │ └── grecon2d.m │ └── imagine │ │ ├── EvalFunctions │ │ ├── fCOV.m │ │ ├── fFWHM.m │ │ ├── fMax.m │ │ ├── fMean.m │ │ ├── fMin.m │ │ ├── fSlopeSteepness.m │ │ ├── fSlopeSteepness2.m │ │ └── fStd.m │ │ ├── colormaps │ │ ├── CubeHelix.m │ │ ├── ExpGray.m │ │ ├── InvGray.m │ │ ├── LogGray.m │ │ ├── OptimalColor.m │ │ ├── PlusMinus.m │ │ ├── french.m │ │ ├── inferno.m │ │ ├── license.txt │ │ ├── magma.m │ │ ├── mylines.mat │ │ ├── plasma.m │ │ └── viridis.m │ │ ├── documentation │ │ └── IMAGINE Users Manual.pdf │ │ ├── icons │ │ ├── Icon.png │ │ ├── clock.png │ │ ├── cogs.png │ │ ├── colormap.png │ │ ├── cursor_arrow.png │ │ ├── doc_delete.png │ │ ├── doc_import.png │ │ ├── dock.png │ │ ├── exchange.png │ │ ├── folder_open.png │ │ ├── grid.png │ │ ├── ic.png │ │ ├── line.png │ │ ├── line1.png │ │ ├── link.png │ │ ├── link1.png │ │ ├── lw.png │ │ ├── mask.png │ │ ├── max.png │ │ ├── min.png │ │ ├── phase.png │ │ ├── record.png │ │ ├── reset.png │ │ ├── rewind.png │ │ ├── rg.png │ │ ├── roi.png │ │ ├── rotate.png │ │ ├── save.png │ │ ├── stop.png │ │ ├── tag.png │ │ ├── undock.png │ │ └── zoom.png │ │ ├── imagine.m │ │ ├── imagineSave.mat │ │ ├── import │ │ ├── fDICOMRead.m │ │ ├── fGIPLRead.m │ │ ├── fMHDRead.m │ │ ├── fMatRead.m │ │ ├── fNifTyRead.m │ │ └── fWSImport.m │ │ ├── license.txt │ │ └── tools │ │ ├── fIsoContour_mex.cpp │ │ ├── fIsoContour_mex.mexmaci64 │ │ ├── fLiveWireCalcP.cpp │ │ ├── fLiveWireCalcP.m │ │ ├── fLiveWireCalcP.mexmaci64 │ │ ├── fLiveWireGetCostFcn.m │ │ ├── fLiveWireGetPath.m │ │ ├── fRegionGrowingAuto_mex.cpp │ │ └── fRegionGrowingAuto_mex.mexmaci64 ├── BFR │ ├── do_LaplacianUnwrapping.m │ ├── do_LaplacianUnwrapping3D.m │ ├── get_LaplaceKernel_imagespace.m │ ├── get_LaplaceOperator_kspace.m │ ├── remove_backgroundField_LBV.m │ └── unwrapLaplacian_fieldmap_Hz.m ├── DI │ ├── MEDI_l1.m │ ├── MEDI_l2_imagespace.m │ ├── closedFormL2.m │ ├── conjugate_gradients │ │ ├── Conjugate_gradient_Test.m │ │ └── conjugate_gradients.m │ ├── depad_array3d.m │ ├── forwardSimulate_RDF_ppm.m │ └── get_dipoleKernel_kspace.m ├── FM │ └── CSS │ │ ├── WFI │ │ ├── FatModel.m │ │ ├── FatModelTest.m │ │ ├── ResidualParamsTest.m │ │ ├── fatModel.csv │ │ ├── find_Extrema.m │ │ ├── finite_difference.m │ │ ├── get_ResidualParams.m │ │ ├── get_VarproResidualParams.m │ │ ├── separate_waterFat.m │ │ └── shift_array.m │ │ └── core │ │ ├── CSS.m │ │ ├── CSS_doc.m │ │ ├── CSS_mex.mexmaci64 │ │ ├── CSSvoxel.m │ │ ├── LICENSE │ │ ├── README.org │ │ ├── README.txt │ │ ├── TestCSS.m │ │ ├── apply_linearUpdates.m │ │ ├── apply_nonlinearUpdates.m │ │ ├── build_signal.m │ │ ├── compute_multiSpeciesHessian.m │ │ ├── compute_multiSpeciesJacobian.m │ │ ├── flatten3d.m │ │ ├── get_CSS_Amatrix.m │ │ ├── plot_residual.m │ │ ├── set_option.m │ │ ├── split_ReIm.m │ │ └── zip.sh ├── LabelStats │ ├── extract_labelstats.py │ └── mySimpleITK.py └── common │ ├── ImDataParamsBFR.m │ ├── ImDataParamsBMRR.m │ ├── ImDataParamsBase.m │ ├── ImDataParamsQSM.m │ ├── ImDataParamsWFI.m │ ├── MyHandle.m │ ├── functions │ ├── FiniteDifferences │ │ ├── compute_backward_difference_gradient.m │ │ ├── compute_backward_divergence.m │ │ ├── compute_central_difference_gradient.m │ │ ├── compute_forward_difference_gradient.m │ │ ├── compute_forward_divergence.m │ │ ├── get_backwardDifferenceOperators_kspace.m │ │ ├── get_backwardFiniteDifferences.m │ │ ├── get_centralDifferenceOperators_kspace.m │ │ ├── get_centralFiniteDifferences.m │ │ ├── get_divGradChi.m │ │ ├── get_divGradOf3dArray.m │ │ ├── get_divOf4dGradArray.m │ │ ├── get_forwardDifferenceOperators_kspace.m │ │ ├── get_forwardFiniteDifferences.m │ │ ├── get_gradChi.m │ │ └── get_gradOf3dArray.m │ ├── addNoise.m │ ├── add_vars2struct.m │ ├── binary_erode.m │ ├── combine_WholeBodyScan_ImDataParams.m │ ├── equalize_fieldmap_periods.m │ ├── fill_mask3D.m │ ├── fit_monoExponentialRelaxation.m │ ├── get_B0dir.m │ ├── get_FOV_mm.m │ ├── get_IPimage.m │ ├── get_ImDataParamsFileCell.m │ ├── get_KsDataParams.m │ ├── get_OPimage.m │ ├── get_T2s_ms.m │ ├── get_affMat_RAF2xyz.m │ ├── get_affineMatrix_DICOMijk2RAFplus.m │ ├── get_affineMatrix_RAFplus2xyz.m │ ├── get_affineMatrix_ijk2RAFplus.m │ ├── get_affineMatrix_ijk2xyz.m │ ├── get_basisGrid.m │ ├── get_center_ijk.m │ ├── get_dTE_s.m │ ├── get_echoMIP.m │ ├── get_fatFraction_percent.m │ ├── get_fieldmap_Hz.m │ ├── get_imDataParams4toolbox.m │ ├── get_magnitude.m │ ├── get_matrixSize.m │ ├── get_openDimension.m │ ├── get_orientationMatrix.m │ ├── get_permMat_RAF2xyz.m │ ├── get_permMat_REC2RAF.m │ ├── get_permMat_convention.m │ ├── get_permMat_mat2RAI.m │ ├── get_permMat_mat2itk.m │ ├── get_phase.m │ ├── get_rotMat_AFR2RAF.m │ ├── get_rotMat_RAF2xyz.m │ ├── get_rotMat_REC2RAF.m │ ├── get_rotMat_dicom2RAI.m │ ├── get_rotationMatrix_APFHRL2RAFplus.m │ ├── get_rotationMatrix_RAFplus2xyz.m │ ├── get_shimShift_Hz.m │ ├── get_tissueMask.m │ ├── phaseDemodulate_field4d_rad.m │ ├── phaseDemodulate_field_Hz.m │ ├── phaseDemodulate_field_T.m │ ├── plot_WFIparams.m │ ├── plot_WFIparamsSlice.m │ ├── reduce_imDataParams2slice.m │ ├── scale_array2interval.m │ ├── show_isoCenter.m │ ├── threshold_array.m │ ├── unpack_struct2vars.m │ └── wrap_fieldmap_Hz.m │ ├── get_GitInfo.m │ └── merge_Structs.m ├── data ├── .gitattributes ├── 20180406_144018_0302_ImDataParams.mat ├── 20180406_144018_0302_bFFEhires.nii.gz └── 20180406_502_CT.nrrd ├── figures ├── CT │ ├── CT.m │ ├── chi.tex │ ├── chi1.tex │ ├── chi2.tex │ ├── ct.tex │ ├── ct1.tex │ ├── ct2.tex │ ├── fig_CT.tex │ ├── fig_CT1.tex │ ├── fig_CT2.tex │ ├── fig_CT3.tex │ ├── fig_CT3_simplified.tex │ ├── fig_CT4.tex │ ├── fig_CT4_simplified.tex │ ├── fig_CT_simplified.tex │ ├── mip.tex │ ├── mip1.tex │ ├── mip2.tex │ ├── r2s.tex │ ├── r2s1.tex │ └── r2s2.tex ├── CTregression │ ├── CT_ROIs_labelstats.csv │ ├── CT_regression.py │ ├── CT_regression_clfl2.py │ ├── CT_regression_l2MEDI.py │ ├── CT_regression_unwrap.py │ ├── draft_regression.tex │ ├── draft_regression_MEDIl2TVcg.tex │ ├── draft_regression_closedFormL2.tex │ ├── draft_regression_unwrap.tex │ ├── fig_CTregression.tex │ ├── fig_CTregression2.tex │ ├── figure.dat │ ├── figure_MEDIl2.dat │ ├── figure_clfl2.dat │ └── figure_unwrap.dat ├── concom │ ├── concom.m │ ├── echoMIP.tex │ ├── lbv.tex │ ├── lbv_cg.tex │ ├── lbv_cg_concom.tex │ ├── lbv_close.tex │ ├── lbv_close_concom.tex │ ├── lbv_concom.tex │ ├── lbv_nesta.tex │ ├── lbv_nesta_concom.tex │ ├── pdf.tex │ ├── pdf_cg.tex │ ├── pdf_cg_concom.tex │ ├── pdf_close.tex │ ├── pdf_close_concom.tex │ ├── pdf_concom.tex │ ├── pdf_nesta.tex │ └── pdf_nesta_concom.tex ├── dipole_inversions │ ├── anatomical_images.tex │ ├── chi_images.tex │ ├── dipole_inversions.m │ ├── dipole_inversions_input.tex │ ├── fig_dipole_inversions.tex │ ├── pdff.tex │ ├── r2s.tex │ └── resample_bssfp.py ├── flowchart │ ├── R2s.tex │ ├── chi.tex │ ├── fig_flowchart.tex │ ├── flowchart.m │ ├── flowchart_input.tex │ ├── local_field_ppm.tex │ ├── pdff.tex │ ├── src.tex │ ├── total_field_Hz.tex │ └── total_field_ppm.tex ├── lcurve │ ├── fig_lcurve.tex │ ├── plot_lcurve.m │ ├── subject01_chi_cg_CSS_LBV_unwrap_11.tex │ ├── subject01_chi_cg_CSS_LBV_unwrap_4.tex │ ├── subject01_chi_cg_CSS_LBV_unwrap_6.tex │ ├── subject01_chi_cg_CSS_PDF_unwrap_11.tex │ ├── subject01_chi_cg_CSS_PDF_unwrap_4.tex │ ├── subject01_chi_cg_CSS_PDF_unwrap_6.tex │ ├── subject01_chi_close_CSS_LBV_unwrap_11.tex │ ├── subject01_chi_close_CSS_LBV_unwrap_4.tex │ ├── subject01_chi_close_CSS_LBV_unwrap_6.tex │ ├── subject01_chi_close_CSS_PDF_unwrap_11.tex │ ├── subject01_chi_close_CSS_PDF_unwrap_4.tex │ ├── subject01_chi_close_CSS_PDF_unwrap_6.tex │ ├── subject01_chi_nesta_CSS_LBV_unwrap_11.tex │ ├── subject01_chi_nesta_CSS_LBV_unwrap_4.tex │ ├── subject01_chi_nesta_CSS_LBV_unwrap_6.tex │ ├── subject01_chi_nesta_CSS_PDF_unwrap_11.tex │ ├── subject01_chi_nesta_CSS_PDF_unwrap_4.tex │ ├── subject01_chi_nesta_CSS_PDF_unwrap_6.tex │ └── subject01_lcurve_plot.tex ├── limitation │ ├── echoMIP.tex │ ├── fig_limitation.tex │ ├── lbv.tex │ ├── lbv_cg.tex │ ├── lbv_close.tex │ ├── lbv_nesta.tex │ ├── limitation.m │ ├── pdf.tex │ ├── pdf_cg.tex │ ├── pdf_close.tex │ └── pdf_nesta.tex ├── multiparam │ ├── chi.tex │ ├── fig_improfiles.tex │ ├── fig_multiparam.tex │ ├── improfiles.csv │ ├── improfiles.tex │ ├── mip.tex │ ├── multiparam.m │ ├── pdff.tex │ └── r2s.tex ├── regression │ ├── create_figure.py │ ├── draft_regression.tex │ ├── draft_regression_MEDIl2TVcg.tex │ ├── draft_regression_MEDIl2TVcg_outlierfree.tex │ ├── draft_regression_closedFormL2.tex │ ├── fig_regression.tex │ ├── fig_regression2.tex │ ├── fig_regression_MEDIl2TVcg.tex │ ├── fig_regression_closedformL2-1.synctex │ ├── fig_regression_closedformL2.tex │ └── figure.dat ├── sim │ ├── P2_B0dir001_nonUTE_R2s.tex │ ├── P2_B0dir001_nonUTE_RDF.tex │ ├── P2_B0dir001_nonUTE_RDF_downsamp.tex │ ├── P2_B0dir001_nonUTE_chi.tex │ ├── P2_B0dir001_nonUTE_mask.tex │ ├── P2_B0dir001_nonUTE_signal.tex │ ├── P2_B0dir001_nonUTE_signal_downsamp.tex │ ├── P4_B0dir001_nonUTE_R2s.tex │ ├── P4_B0dir001_nonUTE_RDF.tex │ ├── P4_B0dir001_nonUTE_RDF_downsamp.tex │ ├── P4_B0dir001_nonUTE_chi.tex │ ├── P4_B0dir001_nonUTE_mask.tex │ ├── P4_B0dir001_nonUTE_signal.tex │ ├── P4_B0dir001_nonUTE_signal_downsamp.tex │ ├── _region_.tex │ ├── fig_sim.tex │ ├── plot.tex │ └── sim.m └── sphere_sim │ ├── bvtv_R2prime_fullvol.tex │ ├── bvtv_meanchi_fullvol.tex │ ├── bvtvchi_dchi05.dat │ ├── bvtvchi_dchi1.dat │ ├── bvtvchi_dchi15.dat │ ├── bvtvchi_dchi2.dat │ ├── fig_grid.tex │ ├── fig_rdfdchi.tex │ ├── fixNchi_dchiR2p.dat │ ├── fixNchi_dchibvtv.dat │ ├── fixNchi_dchibvtv_fit3.dat │ ├── fixNchi_dchichi.dat │ ├── fixNchi_dchichi_fit3.dat │ ├── fixNr_dchiR2p.dat │ ├── fixNr_dchibvtv.dat │ ├── fixNr_dchichi.dat │ ├── fixchir_dchiR2p.dat │ ├── fixchir_dchibvtv.dat │ └── fixchir_dchichi.dat └── scripts ├── BFR_subject.m ├── QSM_subject.m ├── WFI_subject.m ├── demo.m ├── make_nii_subject.m ├── measure_apparentBVTV.py ├── output.png ├── register_mip2bssfp.py ├── resample_echoMIP_labels.py ├── run_N4BiasCorr.py └── run_subject.m /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/maxdiefenbach/trabecular_bone_QSM/HEAD/.gitattributes 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